Publications that acknowledge the role of the NLHPC in their research
2019 |
Lee-Estevez, Manuel; Larama, Giovanni; Figueroa, Elías; Ulloa-Rodríguez, Patricio; Díaz, Rommy; Valdebenito, Iván; Farías, Jorge G Complete mitochondrial genome sequence of Patagonian blenny, Eleginops maclovinus (Perciformes: Eleginopidae) with phylogenetic consideration Journal Article Conservation Genetics Resources, 11 (1), pp. 23–26, 2019, ISSN: 1877-7260. @article{Lee-Estevez2019, title = {Complete mitochondrial genome sequence of Patagonian blenny, Eleginops maclovinus (Perciformes: Eleginopidae) with phylogenetic consideration}, author = {Manuel Lee-Estevez and Giovanni Larama and El\'{i}as Figueroa and Patricio Ulloa-Rodr\'{i}guez and Rommy D\'{i}az and Iv\'{a}n Valdebenito and Jorge G Far\'{i}as}, url = {https://doi.org/10.1007/s12686-017-0954-3}, doi = {10.1007/s12686-017-0954-3}, issn = {1877-7260}, year = {2019}, date = {2019-03-01}, journal = {Conservation Genetics Resources}, volume = {11}, number = {1}, pages = {23--26}, abstract = {Patagonian blenny (Eleginops maclovinus) is the only member of Eleginopidae family. It has been an important resource for Chilean artisanal fishermen communities, however, capture volumes have progressively decreased over last decades likely because overfishing, and concerns for conservation of this species have rised. In this work, mitochondrial DNA of E. maclovinus was fully sequenced using NGS technology. The mitochondrial genome is 16,960 bp long, showing high similarity with other Antarctic fishes. Phylogenetic analysis showed E. maclovinus closer to Nototheniidae and Channichthyidae families within Notothenioidei suborder. As conclusion, we obtained and described the complete mitogenome from E. maclovinus, which constitute a valuable and useful resource for population genetic study and monitoring, as well as for further conservation efforts on this species.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Patagonian blenny (Eleginops maclovinus) is the only member of Eleginopidae family. It has been an important resource for Chilean artisanal fishermen communities, however, capture volumes have progressively decreased over last decades likely because overfishing, and concerns for conservation of this species have rised. In this work, mitochondrial DNA of E. maclovinus was fully sequenced using NGS technology. The mitochondrial genome is 16,960 bp long, showing high similarity with other Antarctic fishes. Phylogenetic analysis showed E. maclovinus closer to Nototheniidae and Channichthyidae families within Notothenioidei suborder. As conclusion, we obtained and described the complete mitogenome from E. maclovinus, which constitute a valuable and useful resource for population genetic study and monitoring, as well as for further conservation efforts on this species. |
á, Rodríguez Ju A; í, Borges-Mart M; ó, Cárdenas-Jir G; Villanueva, Salazar M; Anota, Chigo E Stability, electronic and optical properties of the boron nitride cage (B47N53) from quantum mechanical calculations Journal Article Physica E: Low-dimensional Systems and Nanostructures, 2019. @article{Jurez2019, title = {Stability, electronic and optical properties of the boron nitride cage (B47N53) from quantum mechanical calculations}, author = {Rodr\'{i}guez Ju A \'{a} and Borges-Mart M \'{i} and C\'{a}rdenas-Jir G \'{o} and Salazar M Villanueva and Chigo E Anota}, url = {https://doi.org/10.1016/j.physe.2019.02.017}, doi = {10.1016/j.physe.2019.02.017}, year = {2019}, date = {2019-02-01}, journal = {Physica E: Low-dimensional Systems and Nanostructures}, publisher = {Elsevier BV}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ś, Sylwester; Deniz, Sezer Senol F; ź, Dorota Wo; Ł, ; á, Horacio Pérez-S; ó, José Cer P; Stochmal, Anna; den-Haan Alonso, Helena; Matkowski, Adam; Orhan, Ilkay Erdogan Selective in vitro and in silico cholinesterase inhibitory activity of isoflavones and stilbenes from Belamcandae chinensis rhizoma Journal Article Phytochemistry Letters, 2019. @article{lusarczyk2019, title = {Selective in vitro and in silico cholinesterase inhibitory activity of isoflavones and stilbenes from Belamcandae chinensis rhizoma}, author = {Sylwester \'{S} and Sezer Senol F Deniz and Dorota Wo \'{z} and \L and Horacio P\'{e}rez-S \'{a} and Jos\'{e} Cer P \'{o} and Anna Stochmal and Helena den-Haan Alonso and Adam Matkowski and Ilkay Erdogan Orhan}, url = {https://doi.org/10.1016/j.phytol.2019.02.006}, doi = {10.1016/j.phytol.2019.02.006}, year = {2019}, date = {2019-02-01}, journal = {Phytochemistry Letters}, publisher = {Elsevier BV}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Travisany, Dante; Goles, Eric; Latorre, Mauricio; é, María-Paz Cort; Maass, Alejandro Generation and robustness of Boolean networks to model Clostridium difficile infection Journal Article Natural Computing, 2019. @article{Travisany2019, title = {Generation and robustness of Boolean networks to model Clostridium difficile infection}, author = {Dante Travisany and Eric Goles and Mauricio Latorre and Mar\'{i}a-Paz Cort \'{e} and Alejandro Maass}, url = {https://doi.org/10.1007/s11047-019-09730-0}, doi = {10.1007/s11047-019-09730-0}, year = {2019}, date = {2019-02-01}, journal = {Natural Computing}, publisher = {Springer Nature}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Maza, Felipe; Maldonado, Jonathan; á, Javiera V; Mandakovic, Dinka; Gaete, Alexis; ó, Ver; á, Mauricio Gonz Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability Journal Article Frontiers in Bioengineering and Biotechnology, 7 , 2019. @article{Maza2019, title = {Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability}, author = {Felipe Maza and Jonathan Maldonado and Javiera V \'{a} and Dinka Mandakovic and Alexis Gaete and Ver \'{o} and Mauricio Gonz \'{a}}, url = {https://doi.org/10.3389/fbioe.2019.00010}, doi = {10.3389/fbioe.2019.00010}, year = {2019}, date = {2019-02-01}, journal = {Frontiers in Bioengineering and Biotechnology}, volume = {7}, publisher = {Frontiers Media SA}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Artal, Osvaldo; Pizarro, Oscar; ú, Héctor Sep H The impact of spring-neap tidal-stream cycles in tidal energy assessments in the Chilean Inland Sea Journal Article Renewable Energy, 2019. @article{Artal2019, title = {The impact of spring-neap tidal-stream cycles in tidal energy assessments in the Chilean Inland Sea}, author = {Osvaldo Artal and Oscar Pizarro and H\'{e}ctor Sep H \'{u}}, url = {https://doi.org/10.1016/j.renene.2019.02.092}, doi = {10.1016/j.renene.2019.02.092}, year = {2019}, date = {2019-02-01}, journal = {Renewable Energy}, publisher = {Elsevier BV}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Letelier, Juvenal A; á, Nicol; Ortega, Jaime H Perturbative corrections for the scaling of heat transport in a Hele-Shaw geometry and its application to geological vertical fractures Journal Article Journal of Fluid Mechanics, 864 , pp. 746–767, 2019. @article{Letelier2019, title = {Perturbative corrections for the scaling of heat transport in a Hele-Shaw geometry and its application to geological vertical fractures}, author = {Juvenal A Letelier and Nicol \'{a} and Jaime H Ortega}, url = {https://doi.org/10.1017/jfm.2019.3}, doi = {10.1017/jfm.2019.3}, year = {2019}, date = {2019-02-01}, journal = {Journal of Fluid Mechanics}, volume = {864}, pages = {746--767}, publisher = {Cambridge University Press (CUP)}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Bernales, Maricarmen; Monsalve, Liliam; Ayala-Raso, Anibal; Valdenegro, Monika; Martínez, Juan-Pablo; Travisany, Dante; Defilippi, Bruno; González-Agüero, Mauricio; Cherian, Sam; Fuentes, Lida Expression of two indole-3-acetic acid (IAA)-amido synthetase (GH3) genes during fruit development of raspberry (Rubus idaeus Heritage) Journal Article Scientia Horticulturae, 246 , pp. 168 – 175, 2019, ISSN: 0304-4238. @article{bernales_expression_2019, title = {Expression of two indole-3-acetic acid (IAA)-amido synthetase (GH3) genes during fruit development of raspberry (Rubus idaeus Heritage)}, author = {Maricarmen Bernales and Liliam Monsalve and Anibal Ayala-Raso and Monika Valdenegro and Juan-Pablo Mart\'{i}nez and Dante Travisany and Bruno Defilippi and Mauricio Gonz\'{a}lez-Ag\"{u}ero and Sam Cherian and Lida Fuentes}, url = {http://www.sciencedirect.com/science/article/pii/S0304423818306952}, doi = {https://doi.org/10.1016/j.scienta.2018.09.077}, issn = {0304-4238}, year = {2019}, date = {2019-01-01}, journal = {Scientia Horticulturae}, volume = {246}, pages = {168 -- 175}, abstract = {The conjugation of indole-3-acetic acid (IAA) to amino acids by indole-3-acetic acid (IAA)-amido synthetases (GH3) is an important part of auxin level regulation. However, the auxin conjugation during development of soft fruits such as raspberry is poorly understood. In this study, indole-3-acetic acid (IAA)-amido synthetases in raspberry, designated as RiGH3 (RiGH3.1, RiGH3.5 transcripts) were evaluated during fruit development of raspberry cultivar Rubus idaeus Heritage, and under IAA treatment. The results showed that before to the onset of ripening the fruit size, weight and the expression of IAA-amido synthetase RiGH3.1 transcript levels increased. Then when the fruits attain full development, fruit firmness and titratable acidity decreased, in the contrast to ethylene production and total soluble solids content increasing. However, the RiGH3.5 transcript was found to be expressed primarily in flowers. When compared to untreated control fruit, fruit treated with 1 mM of IAA at white stage, showed an increase of RiGH3.1 transcript during in-vitro assay (10 °C by 18 h). However, no significant change in the levels of RiGH3.5 was observed during IAA treatment. Multiple alignments of the full-length predicted RiGH3.1 protein sequences revealed a high sequence homology with proteins deduced sequences described for other fruit of Rosaceae species. The RiGH3.1 deduced sequence showed the presence of binding motives for IAA and aspartic acid, and indicate that the isolated sequence have the typical motives of GH3.1 protein family. These findings give new insights into the possible role of RiGH3.1 transcripts, and the IAA conjugation (in maintaining the low concentration of free IAA) during raspberry fruit ripening.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The conjugation of indole-3-acetic acid (IAA) to amino acids by indole-3-acetic acid (IAA)-amido synthetases (GH3) is an important part of auxin level regulation. However, the auxin conjugation during development of soft fruits such as raspberry is poorly understood. In this study, indole-3-acetic acid (IAA)-amido synthetases in raspberry, designated as RiGH3 (RiGH3.1, RiGH3.5 transcripts) were evaluated during fruit development of raspberry cultivar Rubus idaeus Heritage, and under IAA treatment. The results showed that before to the onset of ripening the fruit size, weight and the expression of IAA-amido synthetase RiGH3.1 transcript levels increased. Then when the fruits attain full development, fruit firmness and titratable acidity decreased, in the contrast to ethylene production and total soluble solids content increasing. However, the RiGH3.5 transcript was found to be expressed primarily in flowers. When compared to untreated control fruit, fruit treated with 1 mM of IAA at white stage, showed an increase of RiGH3.1 transcript during in-vitro assay (10 °C by 18 h). However, no significant change in the levels of RiGH3.5 was observed during IAA treatment. Multiple alignments of the full-length predicted RiGH3.1 protein sequences revealed a high sequence homology with proteins deduced sequences described for other fruit of Rosaceae species. The RiGH3.1 deduced sequence showed the presence of binding motives for IAA and aspartic acid, and indicate that the isolated sequence have the typical motives of GH3.1 protein family. These findings give new insights into the possible role of RiGH3.1 transcripts, and the IAA conjugation (in maintaining the low concentration of free IAA) during raspberry fruit ripening. |
Díaz, VB; Schleicher, DRG; Bovino, S; Riaz, R; Vanaverbeke, S; Olave, C Impact of radiation backgrounds on the formation of massive black holes Technical Report 2019. @techreport{diaz_impact_2019, title = {Impact of radiation backgrounds on the formation of massive black holes}, author = {VB D\'{i}az and DRG Schleicher and S Bovino and R Riaz and S Vanaverbeke and C Olave}, url = {http://www.swmath.org/software/1046}, year = {2019}, date = {2019-01-01}, abstract = {Resumen / La existencia de agujeros negros supermasivos de mil millones de masas solares a muy alto corri-miento al rojo nos ha motivado a estudiar como estos objetos tan masivos se forman durante los primeros miles de millones de a\~{n}os despu\'{e}s del Big Bang. El modelo mas prometedor que se ha propuesto es el colapso directo de nubes de gas protogal\'{a}cticas. Este escenario requiere altas tasas de acreci\'{o}n para crear r\'{a}pidamente objetos masi-vos y la inhibici\'{o}n del enfriamiento que causa H2, el cu\'{a}l es importante en el proceso de fragmentaci\'{o}n. Estudios recientes mostraron que, si usamos un fondo radiativo fuerte, el hidr\'{o}geno molecular se destruye, favoreciendo las altas tasas de acreci\'{o}n y por lo tanto formando objetos de muy alta masa. En este trabajo estudiamos el impacto de campos de radiaci\'{o}n UV en una nube de gas primordial usando el c\'{o}digo GRADSPH-KROME para investigar el proceso de fragmentaci\'{o}n en escalas de unidades astron\'{o}micas y por lo tanto la formaci\'{o}n de los primeros agujeros negros supermasivos. Encontramos que para suprimir la formaci\'{o}n de H2 es necesario un valor de J21 muy alto, por lo que los agujeros negros de colapso directo no podr\'{i}an explicar la formaci\'{o}n de los primeros agujeros negros supermasivos. Abstract / The presence of supermassive black holes (SMBHs) of a few billion solar masses at very high redshift has motivated us to study how these massive objects formed during the first billion years after the Big Bang. The most promising model that has been proposed to explain this is the direct collapse of protogalactic gas clouds. In this scenario, very high accretion rates are needed to form massive objects early on and the suppression of H2 cooling is important in regulating the fragmentation. Recent studies have shown that if we use a strong radiation background, the hydrogen molecules are destroyed, favoring the high accretion rates and therefore producing objects of very high mass. In this work we study the impact of UV radiation fields in a primordial gas cloud using the recently coupled code GRADSPH-KROME for the modeling of gravitational collapse including primordial chemistry to explore the fragmentation in AU scales and hence the formation of first SMBHs. We found that to suppress the formation of H2 a very high value of J21 is required, because of that we conclude that the direct collapse black holes (DCBHs) are very unlikely to be an explanation for the formation of the first SMBHs.}, keywords = {}, pubstate = {published}, tppubtype = {techreport} } Resumen / La existencia de agujeros negros supermasivos de mil millones de masas solares a muy alto corri-miento al rojo nos ha motivado a estudiar como estos objetos tan masivos se forman durante los primeros miles de millones de años después del Big Bang. El modelo mas prometedor que se ha propuesto es el colapso directo de nubes de gas protogalácticas. Este escenario requiere altas tasas de acreción para crear rápidamente objetos masi-vos y la inhibición del enfriamiento que causa H2, el cuál es importante en el proceso de fragmentación. Estudios recientes mostraron que, si usamos un fondo radiativo fuerte, el hidrógeno molecular se destruye, favoreciendo las altas tasas de acreción y por lo tanto formando objetos de muy alta masa. En este trabajo estudiamos el impacto de campos de radiación UV en una nube de gas primordial usando el código GRADSPH-KROME para investigar el proceso de fragmentación en escalas de unidades astronómicas y por lo tanto la formación de los primeros agujeros negros supermasivos. Encontramos que para suprimir la formación de H2 es necesario un valor de J21 muy alto, por lo que los agujeros negros de colapso directo no podrían explicar la formación de los primeros agujeros negros supermasivos. Abstract / The presence of supermassive black holes (SMBHs) of a few billion solar masses at very high redshift has motivated us to study how these massive objects formed during the first billion years after the Big Bang. The most promising model that has been proposed to explain this is the direct collapse of protogalactic gas clouds. In this scenario, very high accretion rates are needed to form massive objects early on and the suppression of H2 cooling is important in regulating the fragmentation. Recent studies have shown that if we use a strong radiation background, the hydrogen molecules are destroyed, favoring the high accretion rates and therefore producing objects of very high mass. In this work we study the impact of UV radiation fields in a primordial gas cloud using the recently coupled code GRADSPH-KROME for the modeling of gravitational collapse including primordial chemistry to explore the fragmentation in AU scales and hence the formation of first SMBHs. We found that to suppress the formation of H2 a very high value of J21 is required, because of that we conclude that the direct collapse black holes (DCBHs) are very unlikely to be an explanation for the formation of the first SMBHs. |
Davis, Sergio; Loyola, Claudia; Peralta, Joaquín Bayesian statistical modeling of microcanonical melting times at the superheated regime Journal Article Physica A: Statistical Mechanics and its Applications, 515 , pp. 546 – 557, 2019, ISSN: 0378-4371. @article{davis_bayesian_2019, title = {Bayesian statistical modeling of microcanonical melting times at the superheated regime}, author = {Sergio Davis and Claudia Loyola and Joaqu\'{i}n Peralta}, url = {http://www.sciencedirect.com/science/article/pii/S0378437118313037}, doi = {https://doi.org/10.1016/j.physa.2018.09.174}, issn = {0378-4371}, year = {2019}, date = {2019-01-01}, journal = {Physica A: Statistical Mechanics and its Applications}, volume = {515}, pages = {546 -- 557}, abstract = {Homogeneous melting of superheated crystals at constant energy is a dynamical process, believed to be triggered by the accumulation of thermal vacancies and their self-diffusion. From microcanonical simulations we know that if an ideal crystal is prepared at a given kinetic energy, it takes a random time tw until the melting mechanism is actually triggered. In this work we have studied in detail the statistics of tw for melting at different energies by performing a large number of Z-method simulations and applying state-of-the-art methods of Bayesian statistical inference. By focusing on a small system size and short-time tail of the distribution function, we show that tw is actually gamma-distributed rather than exponential (as asserted in a previous work), with decreasing probability near tw∼0. We also explicitly incorporate in our model the unavoidable truncation of the distribution function due to the limited total time span of a Z-method simulation. The probabilistic model presented in this work can provide some insight into the dynamical nature of the homogeneous melting process, as well as giving a well-defined practical procedure to incorporate melting times from simulation into the Z-method in order to correct the effect of short simulation times.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Homogeneous melting of superheated crystals at constant energy is a dynamical process, believed to be triggered by the accumulation of thermal vacancies and their self-diffusion. From microcanonical simulations we know that if an ideal crystal is prepared at a given kinetic energy, it takes a random time tw until the melting mechanism is actually triggered. In this work we have studied in detail the statistics of tw for melting at different energies by performing a large number of Z-method simulations and applying state-of-the-art methods of Bayesian statistical inference. By focusing on a small system size and short-time tail of the distribution function, we show that tw is actually gamma-distributed rather than exponential (as asserted in a previous work), with decreasing probability near tw∼0. We also explicitly incorporate in our model the unavoidable truncation of the distribution function due to the limited total time span of a Z-method simulation. The probabilistic model presented in this work can provide some insight into the dynamical nature of the homogeneous melting process, as well as giving a well-defined practical procedure to incorporate melting times from simulation into the Z-method in order to correct the effect of short simulation times. |
Banegas-Luna, Antonio Jesús; Imbernón, Baldomero; Castro, Antonio Llanes; Pérez-Garrido, Alfonso; Cerón-Carrasco, José Pedro; Gesing, Sandra; Merelli, Ivan; D’Agostino, Daniele; Pérez-Sánchez, Horacio Advances in distributed computing with modern drug discovery Journal Article Expert Opinion on Drug Discovery, 14 (1), pp. 9–22, 2019. @article{banegas-luna_advances_2019, title = {Advances in distributed computing with modern drug discovery}, author = {Antonio Jes\'{u}s Banegas-Luna and Baldomero Imbern\'{o}n and Antonio Llanes Castro and Alfonso P\'{e}rez-Garrido and Jos\'{e} Pedro Cer\'{o}n-Carrasco and Sandra Gesing and Ivan Merelli and Daniele D’Agostino and Horacio P\'{e}rez-S\'{a}nchez}, url = {https://doi.org/10.1080/17460441.2019.1552936}, doi = {10.1080/17460441.2019.1552936}, year = {2019}, date = {2019-01-01}, journal = {Expert Opinion on Drug Discovery}, volume = {14}, number = {1}, pages = {9--22}, abstract = {ABSTRACTIntroduction: Computational chemistry dramatically accelerates the drug discovery process and high-performance computing (HPC) can be used to speed up the most expensive calculations. Supporting a local HPC infrastructure is both costly and time-consuming, and, therefore, many research groups are moving from in-house solutions to remote-distributed computing platforms.Areas covered: The authors focus on the use of distributed technologies, solutions, and infrastructures to gain access to HPC capabilities, software tools, and datasets to run the complex simulations required in computational drug discovery (CDD).Expert opinion: The use of computational tools can decrease the time to market of new drugs. HPC has a crucial role in handling the complex algorithms and large volumes of data required to achieve specificity and avoid undesirable side-effects. Distributed computing environments have clear advantages over in-house solutions in terms of cost and sustainability. The use of infrastructures relying on virtualization reduces set-up costs. Distributed computing resources can be difficult to access, although web-based solutions are becoming increasingly available. There is a trade-off between cost-effectiveness and accessibility in using on-demand computing resources rather than free/academic resources. Graphics processing unit computing, with its outstanding parallel computing power, is becoming increasingly important.}, keywords = {}, pubstate = {published}, tppubtype = {article} } ABSTRACTIntroduction: Computational chemistry dramatically accelerates the drug discovery process and high-performance computing (HPC) can be used to speed up the most expensive calculations. Supporting a local HPC infrastructure is both costly and time-consuming, and, therefore, many research groups are moving from in-house solutions to remote-distributed computing platforms.Areas covered: The authors focus on the use of distributed technologies, solutions, and infrastructures to gain access to HPC capabilities, software tools, and datasets to run the complex simulations required in computational drug discovery (CDD).Expert opinion: The use of computational tools can decrease the time to market of new drugs. HPC has a crucial role in handling the complex algorithms and large volumes of data required to achieve specificity and avoid undesirable side-effects. Distributed computing environments have clear advantages over in-house solutions in terms of cost and sustainability. The use of infrastructures relying on virtualization reduces set-up costs. Distributed computing resources can be difficult to access, although web-based solutions are becoming increasingly available. There is a trade-off between cost-effectiveness and accessibility in using on-demand computing resources rather than free/academic resources. Graphics processing unit computing, with its outstanding parallel computing power, is becoming increasingly important. |
Menéndez-Proupin, E; Casanova-Páez, M; Montero-Alejo, A L; Flores, M A; Orellana, W Symmetry and thermodynamics of tellurium vacancies in cadmium telluride Journal Article Physica B: Condensed Matter, 2019, ISSN: 0921-4526. @article{menendez-proupin_symmetry_2019, title = {Symmetry and thermodynamics of tellurium vacancies in cadmium telluride}, author = {E Men\'{e}ndez-Proupin and M Casanova-P\'{a}ez and A L Montero-Alejo and M A Flores and W Orellana}, url = {http://www.sciencedirect.com/science/article/pii/S0921452619300134}, doi = {https://doi.org/10.1016/j.physb.2019.01.013}, issn = {0921-4526}, year = {2019}, date = {2019-01-01}, journal = {Physica B: Condensed Matter}, abstract = {The equilibrium geometries and thermodynamic properties of anion vacancies in cadmium telluride, as predicted by density functional theory, are revisited using semilocal and hybrid density functionals. We find that stable configurations in different charge states can only be found after a systematic search considering several starting geometries. The stable charge states, 0 and 2+, display closed-shell electronic configurations, without deep bandgap levels. The 2 + charge state has a Td symmetry with an outward relaxation, while the neutral state is a mixture of configurations with C2v and C3v symmetries, both with the same energy and a negligible energy barrier. Therefore, the neutral charge state presents an effective Td symmetry. Configurations with different symmetries, e.g., D2d, can exist as metastable states. We show that certain configurations may seem falsely stable due to several facts: the bandgap error of generalized gradient approximation, the k-point sampling used in small supercells, or the use of a restricted set of starting geometries. We believe that the HSE06 hybrid functional allows to obtain accurate formation energies and geometries. We analyze the effect of the spin-orbit coupling and GW quasiparticle corrections to the HSE06 results, and find no qualitative differences. The spin-orbit coupling and GW corrections to the HSE06 energies partially cancel each other. Finally, we investigate the divacancy VCdVTe. The obtained formation energies suggest that isolated tellurium vacancies in neutral charge state can be found only in Te-poor growth conditions, coexisting with divacancies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The equilibrium geometries and thermodynamic properties of anion vacancies in cadmium telluride, as predicted by density functional theory, are revisited using semilocal and hybrid density functionals. We find that stable configurations in different charge states can only be found after a systematic search considering several starting geometries. The stable charge states, 0 and 2+, display closed-shell electronic configurations, without deep bandgap levels. The 2 + charge state has a Td symmetry with an outward relaxation, while the neutral state is a mixture of configurations with C2v and C3v symmetries, both with the same energy and a negligible energy barrier. Therefore, the neutral charge state presents an effective Td symmetry. Configurations with different symmetries, e.g., D2d, can exist as metastable states. We show that certain configurations may seem falsely stable due to several facts: the bandgap error of generalized gradient approximation, the k-point sampling used in small supercells, or the use of a restricted set of starting geometries. We believe that the HSE06 hybrid functional allows to obtain accurate formation energies and geometries. We analyze the effect of the spin-orbit coupling and GW quasiparticle corrections to the HSE06 results, and find no qualitative differences. The spin-orbit coupling and GW corrections to the HSE06 energies partially cancel each other. Finally, we investigate the divacancy VCdVTe. The obtained formation energies suggest that isolated tellurium vacancies in neutral charge state can be found only in Te-poor growth conditions, coexisting with divacancies. |
Martínez-Cifuentes, Maximiliano; Monroy-Cárdenas, Matías; Millas-Vargas, Juan Pablo; Weiss-López, Boris E; Araya-Maturana, Ramiro Assessing Parameter Suitability for the Strength Evaluation of Intramolecular Resonance Assisted Hydrogen Bonding in o-Carbonyl Hydroquinones Journal Article Molecules, 24 (2), 2019, ISSN: 1420-3049. @article{martinez-cifuentes_assessing_2019, title = {Assessing Parameter Suitability for the Strength Evaluation of Intramolecular Resonance Assisted Hydrogen Bonding in o-Carbonyl Hydroquinones}, author = {Maximiliano Mart\'{i}nez-Cifuentes and Mat\'{i}as Monroy-C\'{a}rdenas and Juan Pablo Millas-Vargas and Boris E Weiss-L\'{o}pez and Ramiro Araya-Maturana}, url = {http://www.mdpi.com/1420-3049/24/2/280}, doi = {10.3390/molecules24020280}, issn = {1420-3049}, year = {2019}, date = {2019-01-01}, journal = {Molecules}, volume = {24}, number = {2}, abstract = {Intramolecular hydrogen bond (IMHB) interactions have attracted considerable attention due to their central role in molecular structure, chemical reactivity, and interactions of biologically active molecules. Precise correlations of the strength of IMHB’s with experimental parameters are a key goal in order to model compounds for drug discovery. In this work, we carry out an experimental (NMR) and theoretical (DFT) study of the IMHB in a series of structurally similar o-carbonyl hydroquinones. Geometrical parameters, as well as Natural Bond Orbital (NBO) and Quantum Theory of Atoms in Molecules (QTAIM) parameters for IMHB were compared with experimental NMR data. Three DFT functionals were employed to calculated theoretical parameters: B3LYP, M06-2X, and ωB97XD. O…H distance is the most suitable geometrical parameter to distinguish among similar IMHBs. Second order stabilization energies ΔEij(2) from NBO analysis and hydrogen bond energy (EHB) obtained from QTAIM analysis also properly distinguishes the order in strength of the studied IMHB. ΔEij(2) from NBO give values for the IMHB below 30 kcal/mol, while EHB from QTAIM analysis give values above 30 kcal/mol. In all cases, the calculated parameters using ωB97XD give the best correlations with experimental 1H-NMR chemical shifts for the IMHB, with R2 values around 0.89. Although the results show that these parameters correctly reflect the strength of the IMHB, when the weakest one is removed from the analysis, arguing experimental considerations, correlations improve significantly to values around 0.95 for R2.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Intramolecular hydrogen bond (IMHB) interactions have attracted considerable attention due to their central role in molecular structure, chemical reactivity, and interactions of biologically active molecules. Precise correlations of the strength of IMHB’s with experimental parameters are a key goal in order to model compounds for drug discovery. In this work, we carry out an experimental (NMR) and theoretical (DFT) study of the IMHB in a series of structurally similar o-carbonyl hydroquinones. Geometrical parameters, as well as Natural Bond Orbital (NBO) and Quantum Theory of Atoms in Molecules (QTAIM) parameters for IMHB were compared with experimental NMR data. Three DFT functionals were employed to calculated theoretical parameters: B3LYP, M06-2X, and ωB97XD. O…H distance is the most suitable geometrical parameter to distinguish among similar IMHBs. Second order stabilization energies ΔEij(2) from NBO analysis and hydrogen bond energy (EHB) obtained from QTAIM analysis also properly distinguishes the order in strength of the studied IMHB. ΔEij(2) from NBO give values for the IMHB below 30 kcal/mol, while EHB from QTAIM analysis give values above 30 kcal/mol. In all cases, the calculated parameters using ωB97XD give the best correlations with experimental 1H-NMR chemical shifts for the IMHB, with R2 values around 0.89. Although the results show that these parameters correctly reflect the strength of the IMHB, when the weakest one is removed from the analysis, arguing experimental considerations, correlations improve significantly to values around 0.95 for R2. |
Urzua-Leiva, Rodrigo; Pino-Rios, Ricardo; Cardenas-Jiron, Gloria Phys. Chem. Chem. Phys., pp. –, 2019. @article{urzua-leiva_influence_2019, title = {The Influence of Antenna and Anchoring Moieties on the Improvement of Photoelectronic Properties in Zn(II)-Porphyrin-TiO2 as Potential Dye-Sensitized Solar Cells}, author = {Rodrigo Urzua-Leiva and Ricardo Pino-Rios and Gloria Cardenas-Jiron}, url = {http://dx.doi.org/10.1039/C8CP06988C}, doi = {10.1039/C8CP06988C}, year = {2019}, date = {2019-01-01}, journal = {Phys. Chem. Chem. Phys.}, pages = {--}, abstract = {A systematic study for the rational design of porphyrins (P4 spider-shaped derivatives) with potential application in dye-sensitized solar cells is presented. Using density functional theory (DFT) (B3LYP/6-31G*) and time-dependent DFT (M06/6-31G*) we show that the UV-vis absorption properties of a spider-shaped Zn(II) porphyrin, previously synthesized by Stangel et al., may be greatly improved by applying some push-pull strategies in meso positions. We found that the selected triphenylamine push group induces a remarkable improvement in the absorption bands of P4 spider-shaped derivatives. The pull effect reached through the π-electron-rich phenyl group and the benzodithiazole (BTD) group, allowed the Q bands to be red-shifted up to 689 nm, much longer than the 593 nm reported experimentally for the original spider-shaped porphyrin. The adsorption results of the P4 spider-shaped derivatives onto a TiO2-anatase surface model [Ti16O34H4] through the carboxylic acid group showed that the adsorptions energies were favourable and very similar in all cases. Natural bond orbitals (NBO) indicated a two-center bond (BD) O(carboxyl)-Ti(TiO2) for the porphyrin with the highest adsorption energy (8.27 kcal/mol), and donor acceptor interactions from LP O(carboxyl) to Ti(TiO2) for the other porphyrins. The natural transition orbitals (NTO) for P4-derivatives-TiO2 confirm the nature of the excited states associated with Q and Soret bands. Finally, the frontier molecular orbitals revealed charge-separated states between those occupied and unoccupied, indicating a favourable charge-transfer process between the dyes and the surface conduction bands. In conclusion, this work showed a systematic study based in the push-pull strategy that improves the performance of porphyrins with the purpose to be used in dye-sensitized solar cells.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A systematic study for the rational design of porphyrins (P4 spider-shaped derivatives) with potential application in dye-sensitized solar cells is presented. Using density functional theory (DFT) (B3LYP/6-31G*) and time-dependent DFT (M06/6-31G*) we show that the UV-vis absorption properties of a spider-shaped Zn(II) porphyrin, previously synthesized by Stangel et al., may be greatly improved by applying some push-pull strategies in meso positions. We found that the selected triphenylamine push group induces a remarkable improvement in the absorption bands of P4 spider-shaped derivatives. The pull effect reached through the π-electron-rich phenyl group and the benzodithiazole (BTD) group, allowed the Q bands to be red-shifted up to 689 nm, much longer than the 593 nm reported experimentally for the original spider-shaped porphyrin. The adsorption results of the P4 spider-shaped derivatives onto a TiO2-anatase surface model [Ti16O34H4] through the carboxylic acid group showed that the adsorptions energies were favourable and very similar in all cases. Natural bond orbitals (NBO) indicated a two-center bond (BD) O(carboxyl)-Ti(TiO2) for the porphyrin with the highest adsorption energy (8.27 kcal/mol), and donor acceptor interactions from LP O(carboxyl) to Ti(TiO2) for the other porphyrins. The natural transition orbitals (NTO) for P4-derivatives-TiO2 confirm the nature of the excited states associated with Q and Soret bands. Finally, the frontier molecular orbitals revealed charge-separated states between those occupied and unoccupied, indicating a favourable charge-transfer process between the dyes and the surface conduction bands. In conclusion, this work showed a systematic study based in the push-pull strategy that improves the performance of porphyrins with the purpose to be used in dye-sensitized solar cells. |
Valenzuela, Gerson E Computer Simulation of the Effect of Wetting Conditions on the Solvation Force and Pull-Off Force of Water Confined between Two Flat Substrates Journal Article JOURNAL OF PHYSICAL CHEMISTRY C, 123 (2), pp. 1252–1259, 2019, ISSN: 1932-7447. @article{valenzuela_computer_2019, title = {Computer Simulation of the Effect of Wetting Conditions on the Solvation Force and Pull-Off Force of Water Confined between Two Flat Substrates}, author = {Gerson E Valenzuela}, doi = {10.1021/acs.jpcc.8b09907}, issn = {1932-7447}, year = {2019}, date = {2019-01-01}, journal = {JOURNAL OF PHYSICAL CHEMISTRY C}, volume = {123}, number = {2}, pages = {1252--1259}, abstract = {Modeling experimental results of pull-off versus relative humidity obtained by atomic force microscopy (AFM) has suggested that the classic interaction force models (van der Waals and capillarity) do not capture the water behavior confined between two surfaces at a distance D approximate to 1 nm. In this paper, pull-off generated by bridges of water confined between two flat substrates is studied using molecular dynamics simulations, varying the wetting conditions and the number of water molecules of the bridge. The method used imitates the approach and retraction curves in AFM. The confined water exhibits an oscillatory solvation force for D textless 1.3 nm for both hydrophilic and hydrophobic surfaces. For hydrophilic surfaces, the pull-off corresponds precisely to the maximum of attractive force produced at D approximate to 0.7 nm, where the bridge is composed of two water layers. These results are applicable to the tip-sample nanocontact of experimental systems for substrates at a contact angle textgreater40 degrees.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Modeling experimental results of pull-off versus relative humidity obtained by atomic force microscopy (AFM) has suggested that the classic interaction force models (van der Waals and capillarity) do not capture the water behavior confined between two surfaces at a distance D approximate to 1 nm. In this paper, pull-off generated by bridges of water confined between two flat substrates is studied using molecular dynamics simulations, varying the wetting conditions and the number of water molecules of the bridge. The method used imitates the approach and retraction curves in AFM. The confined water exhibits an oscillatory solvation force for D textless 1.3 nm for both hydrophilic and hydrophobic surfaces. For hydrophilic surfaces, the pull-off corresponds precisely to the maximum of attractive force produced at D approximate to 0.7 nm, where the bridge is composed of two water layers. These results are applicable to the tip-sample nanocontact of experimental systems for substrates at a contact angle textgreater40 degrees. |
Poch, Andrea; Villanelo, Felipe; Henriquez, Soledad; Kohen, Paulina; Muñoz, Alex; Strauss, Jerome F; Devoto, Luigi Molecular modelling predicts that 2-methoxyestradiol disrupts HIF function by binding to the PAS-B domain Journal Article Steroids, 2019, ISSN: 0039-128X. @article{poch_molecular_2019, title = {Molecular modelling predicts that 2-methoxyestradiol disrupts HIF function by binding to the PAS-B domain}, author = {Andrea Poch and Felipe Villanelo and Soledad Henriquez and Paulina Kohen and Alex Mu\~{n}oz and Jerome F Strauss and Luigi Devoto}, url = {http://www.sciencedirect.com/science/article/pii/S0039128X19300212}, doi = {https://doi.org/10.1016/j.steroids.2019.02.004}, issn = {0039-128X}, year = {2019}, date = {2019-01-01}, journal = {Steroids}, abstract = {An estradiol metabolite, 2-methoxyestradiol (2ME), has emerged as an important regulator of ovarian physiology. 2ME is recognized as a potent anti-angiogenic agent in clinical trials and laboratory studies. However, little is known about its molecular actions and its endogenous targets. 2ME is produced by human ovarian cells during the normal menstrual cycle, being higher during regression of the corpus luteum, and is postulated to be involved in the anti-angiogenic process that plays out during luteolysis. We utilized cell biology techniques to understand the molecular mechanism of 2ME anti-angiogenic effects on human granulosa luteal cells. The principal effect of 2ME was to alter Hypoxia Inducible Factor 1A (HIF1A) sub-cellular localization. Molecular modelling and multiple bioinformatics tools indicated that 2ME impairs Hypoxia Inducible Factor complex (HIF) nuclear translocation by binding to a buried pocket in the HIF1A Per Arnt Sim (PAS)-B domain. Binding of 2ME to HIF1A protein is predicted to perturb HIF1A-Hypoxia Inducible Factor B (HIFB) interaction, a key step in HIF nuclear translocation, preventing the transcriptional actions of HIF, including Vascular Endotelial Growth Factor (VEGF) gene activation. To our knowledge, 2ME is the first putative HIF endogenous ligand characterized with anti-angiogenic activity. This postulate has important implications for reproduction, because angiogenic processes are critical for ovarian follicular development, ovulation and corpus luteum regression. The present research could contribute to the development of novel pharmacological approaches for controlling HIF activity in human reproductive diseases.}, keywords = {}, pubstate = {published}, tppubtype = {article} } An estradiol metabolite, 2-methoxyestradiol (2ME), has emerged as an important regulator of ovarian physiology. 2ME is recognized as a potent anti-angiogenic agent in clinical trials and laboratory studies. However, little is known about its molecular actions and its endogenous targets. 2ME is produced by human ovarian cells during the normal menstrual cycle, being higher during regression of the corpus luteum, and is postulated to be involved in the anti-angiogenic process that plays out during luteolysis. We utilized cell biology techniques to understand the molecular mechanism of 2ME anti-angiogenic effects on human granulosa luteal cells. The principal effect of 2ME was to alter Hypoxia Inducible Factor 1A (HIF1A) sub-cellular localization. Molecular modelling and multiple bioinformatics tools indicated that 2ME impairs Hypoxia Inducible Factor complex (HIF) nuclear translocation by binding to a buried pocket in the HIF1A Per Arnt Sim (PAS)-B domain. Binding of 2ME to HIF1A protein is predicted to perturb HIF1A-Hypoxia Inducible Factor B (HIFB) interaction, a key step in HIF nuclear translocation, preventing the transcriptional actions of HIF, including Vascular Endotelial Growth Factor (VEGF) gene activation. To our knowledge, 2ME is the first putative HIF endogenous ligand characterized with anti-angiogenic activity. This postulate has important implications for reproduction, because angiogenic processes are critical for ovarian follicular development, ovulation and corpus luteum regression. The present research could contribute to the development of novel pharmacological approaches for controlling HIF activity in human reproductive diseases. |
Garate, Jose Antonio; Bernardin, Alejandro; Escalona, Yerko; Yañez, Carlos; English, Niall Joseph; Perez-Acle, Tomas Orientational and Folding Thermodynamics via Electric Dipole Moment Restraining Journal Article The Journal of Physical Chemistry B, 2019, ISSN: 1520-6106. @article{garate_orientational_2019, title = {Orientational and Folding Thermodynamics via Electric Dipole Moment Restraining}, author = {Jose Antonio Garate and Alejandro Bernardin and Yerko Escalona and Carlos Ya\~{n}ez and Niall Joseph English and Tomas Perez-Acle}, url = {https://doi.org/10.1021/acs.jpcb.8b09374}, doi = {10.1021/acs.jpcb.8b09374}, issn = {1520-6106}, year = {2019}, date = {2019-01-01}, journal = {The Journal of Physical Chemistry B}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Morell, Suárez E; León, Andrea; Miwa, Hiroki R; Vargas, P Control of magnetism in bilayer CrI3 by an external electric field Journal Article 2D Materials, 6 (2), pp. 025020, 2019. @article{morell_control_2019, title = {Control of magnetism in bilayer CrI3 by an external electric field}, author = {Su\'{a}rez E Morell and Andrea Le\'{o}n and Hiroki R Miwa and P Vargas}, url = {https://doi.org/10.1088%2F2053-1583%2Fab04fb}, doi = {10.1088/2053-1583/ab04fb}, year = {2019}, date = {2019-01-01}, journal = {2D Materials}, volume = {6}, number = {2}, pages = {025020}, abstract = {Recently intrinsic ferromagnetism in two-dimensional(2D) van der Waals materials was discovered (Huang et al 2017 Nature 546 270\textendash3; Gong et al 2017 Nature 546 265\textendash9; O’Hara et al 2018 Nano Lett. 18 3125\textendash31). A monolayer of Chromiun triiodide(CrI3) is ferromagnetic while a bilayer structure was reported to be anti-ferromagnetic, moreover an external electric field changes its magnetic phase (Jiang et al 2018 Nat. Mater. 17 406\textendash10). We have studied the two found in nature stackings of CrI3 bilayers and found that indeed the magnetic phase of one of them can be tuned by an external electric field while the other remains ferromagnetic. We simulate those results with ab initio calculations and explain them with a simple model based on a rigid shift of the bands associated with different spins. The model can be applied to similar van der Waal stacked insulating bilayer anti-ferromagnets.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recently intrinsic ferromagnetism in two-dimensional(2D) van der Waals materials was discovered (Huang et al 2017 Nature 546 270–3; Gong et al 2017 Nature 546 265–9; O’Hara et al 2018 Nano Lett. 18 3125–31). A monolayer of Chromiun triiodide(CrI3) is ferromagnetic while a bilayer structure was reported to be anti-ferromagnetic, moreover an external electric field changes its magnetic phase (Jiang et al 2018 Nat. Mater. 17 406–10). We have studied the two found in nature stackings of CrI3 bilayers and found that indeed the magnetic phase of one of them can be tuned by an external electric field while the other remains ferromagnetic. We simulate those results with ab initio calculations and explain them with a simple model based on a rigid shift of the bands associated with different spins. The model can be applied to similar van der Waal stacked insulating bilayer anti-ferromagnets. |
Ríos, Paulina L; Povea, Paula; Cerda-Cavieres, Christopher; Arroyo, Juan L; Morales-Verdejo, Cesar; Abarca, Gabriel; Camarada, María B RSC Advances, 9 (15), pp. 8480–8489, 2019. @article{rios_novel_2019, title = {Novel in situ synthesis of copper nanoparticles supported on reduced graphene oxide and its application as a new catalyst for the decomposition of composite solid propellants}, author = {Paulina L R\'{i}os and Paula Povea and Christopher Cerda-Cavieres and Juan L Arroyo and Cesar Morales-Verdejo and Gabriel Abarca and Mar\'{i}a B Camarada}, url = {http://dx.doi.org/10.1039/C9RA00789J}, doi = {10.1039/C9RA00789J}, year = {2019}, date = {2019-01-01}, journal = {RSC Advances}, volume = {9}, number = {15}, pages = {8480--8489}, abstract = {The catalytic activity of graphene oxide (GO), reduced graphene oxide (rGO), copper nanoparticles (CuNP) and rGO supported copper nanoparticles (rGOtextbarCuNP) was investigated for the thermal decomposition of ammonium perchlorate (AP). GO was synthesized using a methodology based on hydrophilic oxidation, while an environmentally friendly and non-toxic reducing agent, l-ascorbic acid, was applied for the in situ reduction of copper and GO. The supporting rGO reduced the mean size of the copper nanoparticles from approximately 6 to 2 r{A} due to the presence of stabilizing functional groups on the graphitic structure. Theoretical studies through Density Functional Theory revealed the important role of the epoxy and carbonyl groups of rGO on the stabilization of copper. The thermal decomposition process was studied based on DSC and TGA. GO, and rGO did not show a significant catalytic influence in the decomposition of AP. CuNP reduced the decomposition temperature of AP in greater magnitude than rGOtextbarCuNP however, the synergistic effect of the rGO and CuNP increased the energy release significantly.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The catalytic activity of graphene oxide (GO), reduced graphene oxide (rGO), copper nanoparticles (CuNP) and rGO supported copper nanoparticles (rGOtextbarCuNP) was investigated for the thermal decomposition of ammonium perchlorate (AP). GO was synthesized using a methodology based on hydrophilic oxidation, while an environmentally friendly and non-toxic reducing agent, l-ascorbic acid, was applied for the in situ reduction of copper and GO. The supporting rGO reduced the mean size of the copper nanoparticles from approximately 6 to 2 Å due to the presence of stabilizing functional groups on the graphitic structure. Theoretical studies through Density Functional Theory revealed the important role of the epoxy and carbonyl groups of rGO on the stabilization of copper. The thermal decomposition process was studied based on DSC and TGA. GO, and rGO did not show a significant catalytic influence in the decomposition of AP. CuNP reduced the decomposition temperature of AP in greater magnitude than rGOtextbarCuNP however, the synergistic effect of the rGO and CuNP increased the energy release significantly. |
Suazo, Matías; Prieto, Joaquín; Escala, Andrés; Schleicher, Dominik R G The role of gas fragmentation during the formation of supermassive black holes Technical Report 2019. @techreport{suazo_role_2019, title = {The role of gas fragmentation during the formation of supermassive black holes}, author = {Mat\'{i}as Suazo and Joaqu\'{i}n Prieto and Andr\'{e}s Escala and Dominik R G Schleicher}, url = {https://arxiv.org/pdf/1903.03637.pdf}, year = {2019}, date = {2019-01-01}, abstract = {We have performed cosmological hydrodynamic simulations to study the effect of fragmentation on the SMBH seed mass in the direct collapse formation scenario. We considered different background UV intensities, host halo spin, and halo merger histories. Our simulations in low-spin halos, in the presence of a strong UV background are consistent with the Direct Collapse Black Hole model, in which a single massive object ∼ 10 5 M is formed in the center of a proto-galaxy. While in our simulations under the presence of a low UV background, we find fragmentation and the formation of various minor seeds. These fragments have masses of 10 3-10 4 M. These values are significant if we consider the potential mergers between them, and the fact that these minor objects are formed earlier in cosmic time compared to the massive single seeds. In one of our simulations, we observed gas fragmentation even in the presence of a strong UV intensity. Said structure arose in a dark matter halo that formed after various merger episodes, and the one with the highest spin value. The final mass obtained was ∼ 10 5 M in this run. From these results, we conclude that fragmentation in fact produces less massive objects, however, they are still prone to merge. In simulations that formed many fragments, they all approach the most massive one with time. We see no uniqueness in the strength of the UV intensity value required to achieve a DCBH, since it depends in other factors like the system dynamics in our cases.}, keywords = {}, pubstate = {published}, tppubtype = {techreport} } We have performed cosmological hydrodynamic simulations to study the effect of fragmentation on the SMBH seed mass in the direct collapse formation scenario. We considered different background UV intensities, host halo spin, and halo merger histories. Our simulations in low-spin halos, in the presence of a strong UV background are consistent with the Direct Collapse Black Hole model, in which a single massive object ∼ 10 5 M is formed in the center of a proto-galaxy. While in our simulations under the presence of a low UV background, we find fragmentation and the formation of various minor seeds. These fragments have masses of 10 3-10 4 M. These values are significant if we consider the potential mergers between them, and the fact that these minor objects are formed earlier in cosmic time compared to the massive single seeds. In one of our simulations, we observed gas fragmentation even in the presence of a strong UV intensity. Said structure arose in a dark matter halo that formed after various merger episodes, and the one with the highest spin value. The final mass obtained was ∼ 10 5 M in this run. From these results, we conclude that fragmentation in fact produces less massive objects, however, they are still prone to merge. In simulations that formed many fragments, they all approach the most massive one with time. We see no uniqueness in the strength of the UV intensity value required to achieve a DCBH, since it depends in other factors like the system dynamics in our cases. |
Baruteau, Clément; Barraza, Marcelo; Pérez, Sebastián; Casassus, Simon; Dong, Ruobing; Lyra, Wladimir; Marino, Sebastián; Christiaens, Valentin; Zhu, Zhaohuan; Carmona, Andrés; Debras, Florian; Alarcon, Felipe Dust traps in the protoplanetary disc MWC 758: two vortices produced by two giant planets? Technical Report 2019. @techreport{baruteau_dust_2019, title = {Dust traps in the protoplanetary disc MWC 758: two vortices produced by two giant planets?}, author = {Cl\'{e}ment Baruteau and Marcelo Barraza and Sebasti\'{a}n P\'{e}rez and Simon Casassus and Ruobing Dong and Wladimir Lyra and Sebasti\'{a}n Marino and Valentin Christiaens and Zhaohuan Zhu and Andr\'{e}s Carmona and Florian Debras and Felipe Alarcon}, url = {https://arxiv.org/pdf/1903.06537.pdf}, year = {2019}, date = {2019-01-01}, pages = {1--18}, abstract = {Resolved ALMA and VLA observations indicate the existence of two dust traps in the protoplanetary disc MWC 758. By means of 2D gas+dust hydrodynamical simulations post-processed with 3D dust radiative transfer calculations, we show that the spirals in scattered light, the eccentric, asymmetric ring and the crescent-shaped structure in the (sub)millimetre can all be caused by two giant planets: a 1.5-Jupiter mass planet at 35 au (inside the spirals) and a 5-Jupiter mass planet at 140 au (outside the spirals). The outer planet forms a dust-trapping vortex at the inner edge of its gap (at ∼85 au), and the continuum emission of this dust trap reproduces the ALMA and VLA observations well. The outer planet triggers several spiral arms which are similar to those observed in polarised scattered light. The inner planet also forms a vortex at the outer edge of its gap (at ∼50 au), but it decays faster than the vortex induced by the outer planet, as a result of the disc's turbulent viscosity. The vortex decay can explain the eccentric inner ring seen with ALMA as well as the low signal and larger azimuthal spread of this dust trap in VLA observations. Finding the thermal and kinematic signatures of both giant planets could verify the proposed scenario.}, keywords = {}, pubstate = {published}, tppubtype = {techreport} } Resolved ALMA and VLA observations indicate the existence of two dust traps in the protoplanetary disc MWC 758. By means of 2D gas+dust hydrodynamical simulations post-processed with 3D dust radiative transfer calculations, we show that the spirals in scattered light, the eccentric, asymmetric ring and the crescent-shaped structure in the (sub)millimetre can all be caused by two giant planets: a 1.5-Jupiter mass planet at 35 au (inside the spirals) and a 5-Jupiter mass planet at 140 au (outside the spirals). The outer planet forms a dust-trapping vortex at the inner edge of its gap (at ∼85 au), and the continuum emission of this dust trap reproduces the ALMA and VLA observations well. The outer planet triggers several spiral arms which are similar to those observed in polarised scattered light. The inner planet also forms a vortex at the outer edge of its gap (at ∼50 au), but it decays faster than the vortex induced by the outer planet, as a result of the disc's turbulent viscosity. The vortex decay can explain the eccentric inner ring seen with ALMA as well as the low signal and larger azimuthal spread of this dust trap in VLA observations. Finding the thermal and kinematic signatures of both giant planets could verify the proposed scenario. |
Bravo, Silvana; Larama, Giovanni; Quiñones, John; Paz, Erwin; Rodero, Evangelina; Sepúlveda, Néstor Genetic diversity and phylogenetic relationship among araucana creole sheep and Spanish sheep breeds Journal Article Small Ruminant Research, 172 , pp. 23 - 30, 2019, ISSN: 0921-4488. @article{BRAVO201923, title = {Genetic diversity and phylogenetic relationship among araucana creole sheep and Spanish sheep breeds}, author = {Silvana Bravo and Giovanni Larama and John Qui\~{n}ones and Erwin Paz and Evangelina Rodero and N\'{e}stor Sep\'{u}lveda}, url = {http://www.sciencedirect.com/science/article/pii/S0921448819300045}, doi = {https://doi.org/10.1016/j.smallrumres.2019.01.007}, issn = {0921-4488}, year = {2019}, date = {2019-01-01}, journal = {Small Ruminant Research}, volume = {172}, pages = {23 - 30}, abstract = {Knowledge of genetic diversity and relationship among domestic animals is important for sustainable strategies and conservation plans evaluating genetic diversity within and across breeds. Due to the lack of studies focusing on the genetic relationship between the European and South American creole populations, we performed comprehensive genetic analyses of nine sheep breeds raised in Spain compared with Araucana creole sheep. The Araucana creole sheep is an autochthonous breed raised in the south of Chile and represents an important zoogenetic resource for the local economy. The aim of this research was to characterize the genetic variability and structure based on individual genotypes. A total of 179 individuals were analyzed (Ile de France, IF n = 18, Merino Espa\~{n}ol, ME n = 18, Merino de Grazalema, MG n = 16, Merino Negro, MN n = 18, Montesina, MO n = 19, Merino Precoz, MP n = 18, Segure\~{n}a, SE n = 17, Churra Lebrijana, CL n = 14, Fleischschaf, FL n = 13, Araucana, AR n = 28) by using 19 microsatellite markers. In total, 281 alleles were observed, and the value of average polymorphic information content was 0.81. The estimated diversity parameters indicated that populations retained high levels of genetic diversity (0.69 ± 0.06) and revealed the existence of genetic differentiation among the groups (FST = 10.1%). We found that the highest inbreeding coefficient was in the MP (FIS = 0.121). The study also proved the short genetic distance between ME and MG, whereas MO and MP were the most distant populations. Finally, AR presented a short genetic distance with the SE breed. The STRUCTURE analyses revealed that the populations have a particular genetic background and presented different levels of admixture. The most appropriate cluster number was K = 7. This work is the first report to confirm historical information about the genetic origin of the domestic creole population in Chile and its relationship with European breeds. Overall, the population parameters reported here provide useful information for establishing support in terms of decision-making about their conservation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Knowledge of genetic diversity and relationship among domestic animals is important for sustainable strategies and conservation plans evaluating genetic diversity within and across breeds. Due to the lack of studies focusing on the genetic relationship between the European and South American creole populations, we performed comprehensive genetic analyses of nine sheep breeds raised in Spain compared with Araucana creole sheep. The Araucana creole sheep is an autochthonous breed raised in the south of Chile and represents an important zoogenetic resource for the local economy. The aim of this research was to characterize the genetic variability and structure based on individual genotypes. A total of 179 individuals were analyzed (Ile de France, IF n = 18, Merino Español, ME n = 18, Merino de Grazalema, MG n = 16, Merino Negro, MN n = 18, Montesina, MO n = 19, Merino Precoz, MP n = 18, Segureña, SE n = 17, Churra Lebrijana, CL n = 14, Fleischschaf, FL n = 13, Araucana, AR n = 28) by using 19 microsatellite markers. In total, 281 alleles were observed, and the value of average polymorphic information content was 0.81. The estimated diversity parameters indicated that populations retained high levels of genetic diversity (0.69 ± 0.06) and revealed the existence of genetic differentiation among the groups (FST = 10.1%). We found that the highest inbreeding coefficient was in the MP (FIS = 0.121). The study also proved the short genetic distance between ME and MG, whereas MO and MP were the most distant populations. Finally, AR presented a short genetic distance with the SE breed. The STRUCTURE analyses revealed that the populations have a particular genetic background and presented different levels of admixture. The most appropriate cluster number was K = 7. This work is the first report to confirm historical information about the genetic origin of the domestic creole population in Chile and its relationship with European breeds. Overall, the population parameters reported here provide useful information for establishing support in terms of decision-making about their conservation. |
Lagos-Álvarez, Bernardo; Padilla, Leonardo; Mateu, Jorge; Ferreira, Guillermo A Kalman filter method for estimation and prediction of space–time data with an autoregressive structure Journal Article Journal of Statistical Planning and Inference, 2019, ISSN: 0378-3758. @article{lagos-alvarez_kalman_2019, title = {A Kalman filter method for estimation and prediction of space\textendashtime data with an autoregressive structure}, author = {Bernardo Lagos-\'{A}lvarez and Leonardo Padilla and Jorge Mateu and Guillermo Ferreira}, url = {http://www.sciencedirect.com/science/article/pii/S0378375819300278}, doi = {https://doi.org/10.1016/j.jspi.2019.03.005}, issn = {0378-3758}, year = {2019}, date = {2019-01-01}, journal = {Journal of Statistical Planning and Inference}, abstract = {We propose a new Kalman filter algorithm to provide a formal statistical analysis of space\textendashtime data with an autoregressive structure. The Kalman filter technique allows to capture the temporal dependence as well as the spatial correlation structure through state-space equations, and it is aimed to perform statistical inference in terms of both parameter estimation and prediction at unobserved locations. We put in relevance the nugget effect at the observation equation. We test our procedure and compare it with classical kriging prediction via an intensive simulation study. We show that the Kalman filter is superior in both the estimation, without using a plug-in approach, and prediction for spatio-temporal data, providing a suitable formal procedure for the statistical analysis of space\textendashtime data. Finally, an application to the prediction of daily air temperature data in some regions of southern Chile is presented.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We propose a new Kalman filter algorithm to provide a formal statistical analysis of space–time data with an autoregressive structure. The Kalman filter technique allows to capture the temporal dependence as well as the spatial correlation structure through state-space equations, and it is aimed to perform statistical inference in terms of both parameter estimation and prediction at unobserved locations. We put in relevance the nugget effect at the observation equation. We test our procedure and compare it with classical kriging prediction via an intensive simulation study. We show that the Kalman filter is superior in both the estimation, without using a plug-in approach, and prediction for spatio-temporal data, providing a suitable formal procedure for the statistical analysis of space–time data. Finally, an application to the prediction of daily air temperature data in some regions of southern Chile is presented. |
Villegas-Escobar, Nery; Poater, Albert; Solà, Miquel; Schaefer, Henry F; Toro-Labbé, Alejandro Decomposition of the electronic activity in competing [5,6] and [6,6] cycloaddition reactions between C60 and cyclopentadiene Journal Article Phys. Chem. Chem. Phys., 21 (9), pp. 5039–5048, 2019. @article{villegas-escobar_decomposition_2019, title = {Decomposition of the electronic activity in competing [5,6] and [6,6] cycloaddition reactions between C60 and cyclopentadiene}, author = {Nery Villegas-Escobar and Albert Poater and Miquel Sol\`{a} and Henry F Schaefer and Alejandro Toro-Labb\'{e}}, url = {http://dx.doi.org/10.1039/C8CP07626J}, doi = {10.1039/C8CP07626J}, year = {2019}, date = {2019-01-01}, journal = {Phys. Chem. Chem. Phys.}, volume = {21}, number = {9}, pages = {5039--5048}, abstract = {Fullerenes, in particular C60, are important molecular entities in many areas, ranging from material science to medicinal chemistry. However, chemical transformations have to be done in order to transform C60 in added-value compounds with increased applicability. The most common procedure corresponds to the classical Diels\textendashAlder cycloaddition reaction. In this research, a comprehensive study of the electronic activity that takes place in the cycloaddition between C60 and cyclopentadiene toward the [5,6] and [6,6] reaction pathways is presented. These are competitive reaction mechanisms dominated by σ and π fluctuating activity. To better understand the electronic activity at each stage of the mechanism, the reaction force (RF) and the symmetry-adapted reaction electronic flux (SA-REF, JΓi(ξ)) have been used to elucidate whether π or σ bonding changes drive the reaction. Since the studied cycloaddition reaction proceeds through a Cs symmetry reaction path, two SA-REF emerge: JA′(ξ) and JA′′(ξ). In particular, JA′(ξ) mainly accounts for bond transformations associated with π bonds, while JA′′(ξ) is sensitive toward σ bonding changes. It was found that the [6,6] path is highly favored over the [5,6] with respect to activation energies. This difference is primarily due to the less intensive electronic reordering of the σ electrons in the [6,6] path, as a result of the pyramidalization of carbon atoms in C60 (sp2 → sp3 transition). Interestingly, no substantial differences in the π electronic activity from the reactant complex to the transition state structure were found when comparing the [5,6] and [6,6] paths. Partition of the kinetic energy into its symmetry contributions indicates that when a bond is being weakened/broken (formed/strengthened) non-spontaneous (spontaneous) changes in the electronic activity occur, thus prompting an increase (decrease) of the kinetic energy.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Fullerenes, in particular C60, are important molecular entities in many areas, ranging from material science to medicinal chemistry. However, chemical transformations have to be done in order to transform C60 in added-value compounds with increased applicability. The most common procedure corresponds to the classical Diels–Alder cycloaddition reaction. In this research, a comprehensive study of the electronic activity that takes place in the cycloaddition between C60 and cyclopentadiene toward the [5,6] and [6,6] reaction pathways is presented. These are competitive reaction mechanisms dominated by σ and π fluctuating activity. To better understand the electronic activity at each stage of the mechanism, the reaction force (RF) and the symmetry-adapted reaction electronic flux (SA-REF, JΓi(ξ)) have been used to elucidate whether π or σ bonding changes drive the reaction. Since the studied cycloaddition reaction proceeds through a Cs symmetry reaction path, two SA-REF emerge: JA′(ξ) and JA′′(ξ). In particular, JA′(ξ) mainly accounts for bond transformations associated with π bonds, while JA′′(ξ) is sensitive toward σ bonding changes. It was found that the [6,6] path is highly favored over the [5,6] with respect to activation energies. This difference is primarily due to the less intensive electronic reordering of the σ electrons in the [6,6] path, as a result of the pyramidalization of carbon atoms in C60 (sp2 → sp3 transition). Interestingly, no substantial differences in the π electronic activity from the reactant complex to the transition state structure were found when comparing the [5,6] and [6,6] paths. Partition of the kinetic energy into its symmetry contributions indicates that when a bond is being weakened/broken (formed/strengthened) non-spontaneous (spontaneous) changes in the electronic activity occur, thus prompting an increase (decrease) of the kinetic energy. |
Montalva-Medel, Marco; Rica, Sergio; Urbina, Felipe Phase space classification of an Ising Cellular Automaton: the Q2R model Technical Report 2019. @techreport{montalva-medel_phase_2019, title = {Phase space classification of an Ising Cellular Automaton: the Q2R model}, author = {Marco Montalva-Medel and Sergio Rica and Felipe Urbina}, url = {https://arxiv.org/pdf/1903.11761.pdf}, year = {2019}, date = {2019-01-01}, abstract = {An exact characterization of the different dynamical behavior that exhibit the space phase of a reversible and conservative cellular automaton, the so called Q2R model, is shown in this paper. Q2R is a cellular automaton which is a dynamical variation of the Ising model in statistical physics and whose space of configurations grows exponentially with the system size. As a consequence of the intrinsic reversibility of the model, the phase space is composed only by configurations that belong to a fixed point or a limit cycle. In this work we classify them in four types accordingly to well differentiated topological characteristics. Three of them-which we call of type S-I, S-II and S-III-share a symmetry property, while the fourth, which we call of type AS, does not. Specifically, we prove that any configuration of Q2R belongs to one of the four previous limit cycles. Moreover, at a combinatorial level, we are able to determine the number of limit cycles for some small periods which are almost always present in the Q2R. Finally, we provide a general overview of the resulting decomposition of the arbitrary size Q2R phase space, in addition, we realize an exhaustive study of a small Ising system (4 × 4) which is fully analyzed under this new framework.}, keywords = {}, pubstate = {published}, tppubtype = {techreport} } An exact characterization of the different dynamical behavior that exhibit the space phase of a reversible and conservative cellular automaton, the so called Q2R model, is shown in this paper. Q2R is a cellular automaton which is a dynamical variation of the Ising model in statistical physics and whose space of configurations grows exponentially with the system size. As a consequence of the intrinsic reversibility of the model, the phase space is composed only by configurations that belong to a fixed point or a limit cycle. In this work we classify them in four types accordingly to well differentiated topological characteristics. Three of them-which we call of type S-I, S-II and S-III-share a symmetry property, while the fourth, which we call of type AS, does not. Specifically, we prove that any configuration of Q2R belongs to one of the four previous limit cycles. Moreover, at a combinatorial level, we are able to determine the number of limit cycles for some small periods which are almost always present in the Q2R. Finally, we provide a general overview of the resulting decomposition of the arbitrary size Q2R phase space, in addition, we realize an exhaustive study of a small Ising system (4 × 4) which is fully analyzed under this new framework. |
Ley, Francisco; Riquelme, Mario; Sironi, Lorenzo; Verscharen, Daniel; Sandoval, Astor Stochastic ion acceleration by the ion-cyclotron instability in a growing magnetic field Technical Report 2019. @techreport{ley_stochastic_2019, title = {Stochastic ion acceleration by the ion-cyclotron instability in a growing magnetic field}, author = {Francisco Ley and Mario Riquelme and Lorenzo Sironi and Daniel Verscharen and Astor Sandoval}, url = {https://arxiv.org/pdf/1903.11238.pdf}, year = {2019}, date = {2019-01-01}, abstract = {Using 1D and 2D particle-in-cell (PIC) simulations of a plasma with a growing magnetic field B, we show that ions can be stochastically accelerated by the ion-cyclotron (IC) instability. As B grows, an ion pressure anisotropy p ⊥,i textbackslashtextgreater p textbartextbar,i arises, due to the adiabatic invariance of the ion magnetic moment (p textbartextbar,i and p ⊥,i are the ion pressures parallel and perpendicular to B). When initially β i = 0.5 (β i ≡ 8πp i /textbarBtextbar 2 , where p i is the ion isotropic pressure), the pressure anisotropy is limited mainly by inelastic pitch-angle scattering provided by the IC instability, which in turn produces a non-thermal tail in the ion energy spectrum. After B is amplified by a factor ∼ 2.7, this tail can be approximated as a power-law of index ∼ 3.4 plus two non-thermal bumps, and accounts for 2 − 3% of the ions and ∼ 18% of their kinetic energy. On the contrary, when initially β i = 2, the ion scattering is dominated by the mirror instability and the acceleration is suppressed. This implies that efficient ion acceleration requires that initially β i 1. Although we focus on cases where B is amplified by plasma shear, we check that the acceleration occurs similarly if B grows due to plasma compression. Our results are valid in a sub-relativistic regime where the ion thermal energy is ∼ 10% of the ion rest mass energy. This acceleration process can thus be relevant in the inner region of low-luminosity accretion flows around black holes.}, keywords = {}, pubstate = {published}, tppubtype = {techreport} } Using 1D and 2D particle-in-cell (PIC) simulations of a plasma with a growing magnetic field B, we show that ions can be stochastically accelerated by the ion-cyclotron (IC) instability. As B grows, an ion pressure anisotropy p ⊥,i textbackslashtextgreater p textbartextbar,i arises, due to the adiabatic invariance of the ion magnetic moment (p textbartextbar,i and p ⊥,i are the ion pressures parallel and perpendicular to B). When initially β i = 0.5 (β i ≡ 8πp i /textbarBtextbar 2 , where p i is the ion isotropic pressure), the pressure anisotropy is limited mainly by inelastic pitch-angle scattering provided by the IC instability, which in turn produces a non-thermal tail in the ion energy spectrum. After B is amplified by a factor ∼ 2.7, this tail can be approximated as a power-law of index ∼ 3.4 plus two non-thermal bumps, and accounts for 2 − 3% of the ions and ∼ 18% of their kinetic energy. On the contrary, when initially β i = 2, the ion scattering is dominated by the mirror instability and the acceleration is suppressed. This implies that efficient ion acceleration requires that initially β i 1. Although we focus on cases where B is amplified by plasma shear, we check that the acceleration occurs similarly if B grows due to plasma compression. Our results are valid in a sub-relativistic regime where the ion thermal energy is ∼ 10% of the ion rest mass energy. This acceleration process can thus be relevant in the inner region of low-luminosity accretion flows around black holes. |
Medina, Exequiel; Villalobos, Pablo; Coñuecar, Ricardo; Ramírez-Sarmiento, César A; Babul, Jorge The protonation state of an evolutionarily conserved histidine modulates domainswapping stability of FoxP1 Journal Article Scientific Reports, 9 (1), pp. 5441, 2019, ISSN: 2045-2322. @article{medina_protonation_2019, title = {The protonation state of an evolutionarily conserved histidine modulates domainswapping stability of FoxP1}, author = {Exequiel Medina and Pablo Villalobos and Ricardo Co\~{n}uecar and C\'{e}sar A Ram\'{i}rez-Sarmiento and Jorge Babul}, url = {https://doi.org/10.1038/s41598-019-41819-5}, doi = {10.1038/s41598-019-41819-5}, issn = {2045-2322}, year = {2019}, date = {2019-01-01}, journal = {Scientific Reports}, volume = {9}, number = {1}, pages = {5441}, abstract = {Forkhead box P (FoxP) proteins are members of the versatile Fox transcription factors, which control the timing and expression of multiple genes for eukaryotic cell homeostasis. Compared to other Fox proteins, they can form domain-swapped dimers through their DNA-binding \textendashforkhead\textendash domains, enabling spatial reorganization of distant chromosome elements by tethering two DNA molecules together. Yet, domain swapping stability and DNA binding affinity varies between different FoxP proteins. Experimental evidence suggests that the protonation state of a histidine residue conserved in all Fox proteins is responsible for pH-dependent modulation of these interactions. Here, we explore the consequences of the protonation state of another histidine (H59), only conserved within FoxM/O/P subfamilies, on folding and dimerization of the forkhead domain of human FoxP1. Dimer dissociation kinetics and equilibrium unfolding experiments demonstrate that protonation of H59 leads to destabilization of the domain-swapped dimer due to an increase in free energy difference between the monomeric and transition states. This pH\textendashdependence is abolished when H59 is mutated to alanine. Furthermore, anisotropy measurements and molecular dynamics evidence that H59 has a direct impact in the local stability of helix H3. Altogether, our results highlight the relevance of H59 in domain swapping and folding stability of FoxP1.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Forkhead box P (FoxP) proteins are members of the versatile Fox transcription factors, which control the timing and expression of multiple genes for eukaryotic cell homeostasis. Compared to other Fox proteins, they can form domain-swapped dimers through their DNA-binding –forkhead– domains, enabling spatial reorganization of distant chromosome elements by tethering two DNA molecules together. Yet, domain swapping stability and DNA binding affinity varies between different FoxP proteins. Experimental evidence suggests that the protonation state of a histidine residue conserved in all Fox proteins is responsible for pH-dependent modulation of these interactions. Here, we explore the consequences of the protonation state of another histidine (H59), only conserved within FoxM/O/P subfamilies, on folding and dimerization of the forkhead domain of human FoxP1. Dimer dissociation kinetics and equilibrium unfolding experiments demonstrate that protonation of H59 leads to destabilization of the domain-swapped dimer due to an increase in free energy difference between the monomeric and transition states. This pH–dependence is abolished when H59 is mutated to alanine. Furthermore, anisotropy measurements and molecular dynamics evidence that H59 has a direct impact in the local stability of helix H3. Altogether, our results highlight the relevance of H59 in domain swapping and folding stability of FoxP1. |
Stalevski, Marko; Tristram, Konrad R W; Asmus, Daniel Dissecting the active galactic nucleus in Circinus – II. A thin dusty disc and a polar outflow on parsec scales Journal Article Monthly Notices of the Royal Astronomical Society, 484 (3), pp. 3334-3355, 2019, ISSN: 0035-8711. @article{10.1093/mnras/stz220, title = {Dissecting the active galactic nucleus in Circinus \textendash II. A thin dusty disc and a polar outflow on parsec scales}, author = {Marko Stalevski and Konrad R W Tristram and Daniel Asmus}, url = {https://doi.org/10.1093/mnras/stz220}, doi = {10.1093/mnras/stz220}, issn = {0035-8711}, year = {2019}, date = {2019-01-01}, journal = {Monthly Notices of the Royal Astronomical Society}, volume = {484}, number = {3}, pages = {3334-3355}, abstract = {Recent observations which resolved the mid-infrared (MIR) emission of nearby active galactic nuclei (AGNs), surprisingly revealed that their dust emission appears prominently extended in the polar direction, at odds with the expectations from the canonical dusty torus. This polar dust, tentatively associated with dusty winds driven by radiation pressure, is found to have a major contribution to the MIR flux from scales of a few to hundreds of parsecs. When facing a potential change of paradigm, case studies of objects with the best intrinsic resolution are essential. One such source with a clear detection of polar dust is a nearby, well-known AGN in the Circinus galaxy. In the first paper, we successfully explained the peculiar MIR morphology of Circinus observed on large, tens of parsec scales with a model consisting of a compact dusty disc and an extended hollow dusty cone. In this work, we further refine the model on smaller, parsecs scales to test whether it can also explain the MIR interferometric data. We find that a model composed of a thin dusty disc seen almost edge-on and a polar outflow in the form of a hyperboloid shell can reproduce well the VLTI/MIDI observations at all wavelengths, baselines, and position angles. In contrast, while providing a good fit to the integrated MIR spectrum, the dusty torus model fails to reproduce the spatially resolved interferometric data. We put forth the disc + hyperboloid wind model of Circinus AGN as a prototype for the dust structure in the AGN population with polar dust.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Recent observations which resolved the mid-infrared (MIR) emission of nearby active galactic nuclei (AGNs), surprisingly revealed that their dust emission appears prominently extended in the polar direction, at odds with the expectations from the canonical dusty torus. This polar dust, tentatively associated with dusty winds driven by radiation pressure, is found to have a major contribution to the MIR flux from scales of a few to hundreds of parsecs. When facing a potential change of paradigm, case studies of objects with the best intrinsic resolution are essential. One such source with a clear detection of polar dust is a nearby, well-known AGN in the Circinus galaxy. In the first paper, we successfully explained the peculiar MIR morphology of Circinus observed on large, tens of parsec scales with a model consisting of a compact dusty disc and an extended hollow dusty cone. In this work, we further refine the model on smaller, parsecs scales to test whether it can also explain the MIR interferometric data. We find that a model composed of a thin dusty disc seen almost edge-on and a polar outflow in the form of a hyperboloid shell can reproduce well the VLTI/MIDI observations at all wavelengths, baselines, and position angles. In contrast, while providing a good fit to the integrated MIR spectrum, the dusty torus model fails to reproduce the spatially resolved interferometric data. We put forth the disc + hyperboloid wind model of Circinus AGN as a prototype for the dust structure in the AGN population with polar dust. |
Gajardo, Daniel; Escauriaza, Cristián; Ingram, David M Capturing the development and interactions of wakes in tidal turbine arrays using a coupled BEM-DES model Journal Article Ocean Engineering, 181 , pp. 71 - 88, 2019, ISSN: 0029-8018. @article{GAJARDO201971, title = {Capturing the development and interactions of wakes in tidal turbine arrays using a coupled BEM-DES model}, author = {Daniel Gajardo and Cristi\'{a}n Escauriaza and David M Ingram}, url = {http://www.sciencedirect.com/science/article/pii/S0029801819301532}, doi = {https://doi.org/10.1016/j.oceaneng.2019.03.064}, issn = {0029-8018}, year = {2019}, date = {2019-01-01}, journal = {Ocean Engineering}, volume = {181}, pages = {71 - 88}, abstract = {As tidal and hydrokinetic energy systems develop, new tools are needed to assess quantitatively the effects of turbines on the environment and to estimate their performance. When installed in an array, turbine wakes interact, increasing the complexity of the flow and changing their performance. Experimental and numerical approaches have been employed to analyze flows with multiple turbines, but it is not yet clear which level of detail is necessary to represent the flow hydrodynamics and the details of the devices. In numerical approaches, questions remain on the selection of turbulence models and turbine representations, since more realistic but computationally expensive methodologies not necessarily produce an improvement on the understanding of these flows. In this investigation we perform simulations of turbine arrays to study the hydrodynamics of wakes and their interactions, comparing with experiments and previous simulations. We propose a methodology that couples detached-eddy simulations (DES) with Blade Element Momentum (BEM), showing that by capturing the dynamically-rich coherent structures of the flow, we improve the description of mean quantities and turbine performance. The results show that for downstream turbines, there is an accelerated wake development, increasing the temporal variability of the bed shear stress, and the power and thrust coefficients.}, keywords = {}, pubstate = {published}, tppubtype = {article} } As tidal and hydrokinetic energy systems develop, new tools are needed to assess quantitatively the effects of turbines on the environment and to estimate their performance. When installed in an array, turbine wakes interact, increasing the complexity of the flow and changing their performance. Experimental and numerical approaches have been employed to analyze flows with multiple turbines, but it is not yet clear which level of detail is necessary to represent the flow hydrodynamics and the details of the devices. In numerical approaches, questions remain on the selection of turbulence models and turbine representations, since more realistic but computationally expensive methodologies not necessarily produce an improvement on the understanding of these flows. In this investigation we perform simulations of turbine arrays to study the hydrodynamics of wakes and their interactions, comparing with experiments and previous simulations. We propose a methodology that couples detached-eddy simulations (DES) with Blade Element Momentum (BEM), showing that by capturing the dynamically-rich coherent structures of the flow, we improve the description of mean quantities and turbine performance. The results show that for downstream turbines, there is an accelerated wake development, increasing the temporal variability of the bed shear stress, and the power and thrust coefficients. |
Echeverri, Andrea; Gomez, Tatiana; Hadad, C Z Ammonia borane dehydrogenation tendencies using Pt4, Au4, and Pt2Au2 clusters as catalysts Journal Article Molecular Catalysis, 471 , pp. 9 - 20, 2019, ISSN: 2468-8231. @article{ECHEVERRI20199, title = {Ammonia borane dehydrogenation tendencies using Pt4, Au4, and Pt2Au2 clusters as catalysts}, author = {Andrea Echeverri and Tatiana Gomez and C Z Hadad}, url = {http://www.sciencedirect.com/science/article/pii/S2468823119301713}, doi = {https://doi.org/10.1016/j.mcat.2019.04.012}, issn = {2468-8231}, year = {2019}, date = {2019-01-01}, journal = {Molecular Catalysis}, volume = {471}, pages = {9 - 20}, abstract = {Small metallic clusters -mediated gas phase catalysis studies give lights to understand simple and complex catalytic processes, and help in the discovery and explanation of non-traditional “molecular-scale” catalytic systems. In this framework and in the context of clean energy sources based on hydrogen, a comparative study about ammonia borane (AB = NH3BH3) dehydrogenation tendencies, using Pt4, Au4, and Pt2Au2 clusters as catalysts, is made. Molecular details on thermal, kinetic (mechanistic) and reactivity factors are revealed. Our results indicate that all the metal tetramers studied here tends to dehydrogenate the ammonia borane molecule, being the processes exothermic, exergonic and fast. Among the studied catalysts, Pt2Au2 shows the best results, because is capable of easily detach several hydrogen atoms, with high probability of taking them out simultaneously, both from B and N, which helps in avoiding the breakage of B\textendashN bond of AB, what is known to produce the poisoning of the catalyst by ammonia generation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Small metallic clusters -mediated gas phase catalysis studies give lights to understand simple and complex catalytic processes, and help in the discovery and explanation of non-traditional “molecular-scale” catalytic systems. In this framework and in the context of clean energy sources based on hydrogen, a comparative study about ammonia borane (AB = NH3BH3) dehydrogenation tendencies, using Pt4, Au4, and Pt2Au2 clusters as catalysts, is made. Molecular details on thermal, kinetic (mechanistic) and reactivity factors are revealed. Our results indicate that all the metal tetramers studied here tends to dehydrogenate the ammonia borane molecule, being the processes exothermic, exergonic and fast. Among the studied catalysts, Pt2Au2 shows the best results, because is capable of easily detach several hydrogen atoms, with high probability of taking them out simultaneously, both from B and N, which helps in avoiding the breakage of B–N bond of AB, what is known to produce the poisoning of the catalyst by ammonia generation. |
2018 |
Shene, Carolina; Garcés, Marcelo; Vergara, Daniela; ñ, Jhonatan Pe; Claverol, Stéphane; Rubilar, Mónica; Leyton, Allison Production of Lipids and Proteome Variation in a Chilean Thraustochytrium striatum Strain Cultured under Different Growth Conditions Journal Article Marine Biotechnology, 2018, ISSN: 1436-2236. @article{Shene2018, title = {Production of Lipids and Proteome Variation in a Chilean Thraustochytrium striatum Strain Cultured under Different Growth Conditions}, author = {Carolina Shene and Marcelo Garc\'{e}s and Daniela Vergara and Jhonatan Pe{\~{n}}a and St\'{e}phane Claverol and M\'{o}nica Rubilar and Allison Leyton}, url = {https://doi.org/10.1007/s10126-018-9863-z}, doi = {10.1007/s10126-018-9863-z}, issn = {1436-2236}, year = {2018}, date = {2018-11-19}, journal = {Marine Biotechnology}, abstract = {Total lipids and docosahexaenoic acid (DHA) production by a Chilean isolated thraustochytrid were evaluated under different growth conditions in shake flasks. The analyzed strain was identified as Thraustochytrium striatum according to an 18S rRNA gene sequence analysis. The strain (T. striatum AL16) showed negligible growth in media prepared with artificial seawater at concentrations lower than 50% v/v and pH lower than 5. Maltose and starch were better carbon sources for growth than glucose. DHA content of the biomass grown with maltose (60 g L−1) was doubled by increasing the agitation rate from 150 to 250 rpm. The DHA (0.8--6%) and eicosapentaenoic acid (0.2--21%) content in the total lipids varied depending on culture conditions and culture age. Lipid and DHA concentration increased (up to 5 g L−1 and 66 mg L−1, respectively) by regularly feeding the culture with a concentrated starch solution. Carotenoid accumulation was detected in cells grown with maltose or starch. Contrasting conditions of starch and glucose cultures were selected for comparative proteomics. Total protein extracts were separated by two-dimensional gel electrophoresis; 25 spots were identified using ESI-MS/MS. A protein database (143,006 entries) for proteomic interrogation was generated using de novo assembling of Thraustochytrium sp. LLF1b -- MMETSP0199_2 transcriptome; 18 proteins differentially expressed were identified. Three ATP synthases were differentially accumulated in cultures with glucose, whereas malate dehydrogenase was more abundant in cells cultured with starch.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Total lipids and docosahexaenoic acid (DHA) production by a Chilean isolated thraustochytrid were evaluated under different growth conditions in shake flasks. The analyzed strain was identified as Thraustochytrium striatum according to an 18S rRNA gene sequence analysis. The strain (T. striatum AL16) showed negligible growth in media prepared with artificial seawater at concentrations lower than 50% v/v and pH lower than 5. Maltose and starch were better carbon sources for growth than glucose. DHA content of the biomass grown with maltose (60 g L−1) was doubled by increasing the agitation rate from 150 to 250 rpm. The DHA (0.8--6%) and eicosapentaenoic acid (0.2--21%) content in the total lipids varied depending on culture conditions and culture age. Lipid and DHA concentration increased (up to 5 g L−1 and 66 mg L−1, respectively) by regularly feeding the culture with a concentrated starch solution. Carotenoid accumulation was detected in cells grown with maltose or starch. Contrasting conditions of starch and glucose cultures were selected for comparative proteomics. Total protein extracts were separated by two-dimensional gel electrophoresis; 25 spots were identified using ESI-MS/MS. A protein database (143,006 entries) for proteomic interrogation was generated using de novo assembling of Thraustochytrium sp. LLF1b -- MMETSP0199_2 transcriptome; 18 proteins differentially expressed were identified. Three ATP synthases were differentially accumulated in cultures with glucose, whereas malate dehydrogenase was more abundant in cells cultured with starch. |
José, ; Raúl, ; Suárez, Francisco Exploring the interactions between hydrodynamics and fouling in membrane distillation systems – A multiscale approach using CFD Journal Article Desalination, 444 , pp. 63–74, 2018. @article{Amigo2018, title = {Exploring the interactions between hydrodynamics and fouling in membrane distillation systems \textendash A multiscale approach using CFD}, author = {Jos\'{e} and Ra\'{u}l and Francisco Su\'{a}rez}, url = {https://doi.org/10.1016/j.desal.2018.07.009}, doi = {10.1016/j.desal.2018.07.009}, year = {2018}, date = {2018-10-01}, journal = {Desalination}, volume = {444}, pages = {63--74}, publisher = {Elsevier BV}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
ú, Fabián Díaz-N; Quezada, Franco; á, Óscar C V The knapsack problem with scheduled items Journal Article Electronic Notes in Discrete Mathematics, 69 , pp. 293–300, 2018. @article{DazNez2018, title = {The knapsack problem with scheduled items}, author = {Fabi\'{a}n D\'{i}az-N{\'{u}} \~{n} and Franco Quezada and \'{O}scar C V \'{a}}, url = {https://doi.org/10.1016/j.endm.2018.07.038}, doi = {10.1016/j.endm.2018.07.038}, year = {2018}, date = {2018-08-01}, journal = {Electronic Notes in Discrete Mathematics}, volume = {69}, pages = {293--300}, publisher = {Elsevier BV}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
é, Diego Cort; Ortega, Daniela E Effects on the aromatic character of DNA/RNA nucleobases due to its adsorption onto graphene Journal Article International Journal of Quantum Chemistry, pp. e25699, 2018. @article{CortsArriagada2018, title = {Effects on the aromatic character of DNA/RNA nucleobases due to its adsorption onto graphene}, author = {Diego Cort \'{e} and Daniela E Ortega}, url = {https://doi.org/10.1002/qua.25699}, doi = {10.1002/qua.25699}, year = {2018}, date = {2018-08-01}, journal = {International Journal of Quantum Chemistry}, pages = {e25699}, publisher = {Wiley}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Vargas, Brenda; ú, Ra; á, Joelis Rodríguez-Hern; Gembicky, Milan; Xie, Haomiao; é, José Jim; Liu, Yi-Sheng; é, Eduardo Men; Dunbar, Kim R; Lopez, Nazario; Olalde-Velasco, Paul; Solis-Ibarra, Diego Optical, Electronic and Magnetic Engineering of 〈111〉 Layered Halide Perovskites Journal Article Chemistry of Materials, 2018. @article{Vargas2018, title = {Optical, Electronic and Magnetic Engineering of 〈111〉 Layered Halide Perovskites}, author = {Brenda Vargas and Ra \'{u} and Joelis Rodr\'{i}guez-Hern \'{a} and Milan Gembicky and Haomiao Xie and Jos\'{e} Jim \'{e} and Yi-Sheng Liu and Eduardo Men \'{e} and Kim R Dunbar and Nazario Lopez and Paul Olalde-Velasco and Diego Solis-Ibarra}, url = {https://doi.org/10.1021/acs.chemmater.8b02099}, doi = {10.1021/acs.chemmater.8b02099}, year = {2018}, date = {2018-07-01}, journal = {Chemistry of Materials}, publisher = {American Chemical Society (ACS)}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Riaz, R; Vanaverbeke, S; Schleicher, D R G Episodic accretion in binary protostars emerging from self-gravitating solar mass cores Journal Article Astronomy & Astrophysics, 614 , pp. A53, 2018. @article{Riaz2018, title = {Episodic accretion in binary protostars emerging from self-gravitating solar mass cores}, author = {R Riaz and S Vanaverbeke and D R G Schleicher}, url = {https://doi.org/10.1051/0004-6361/201732076}, doi = {10.1051/0004-6361/201732076}, year = {2018}, date = {2018-06-01}, journal = {Astronomy & Astrophysics}, volume = {614}, pages = {A53}, publisher = {EDP Sciences}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pereira, Jordi The robust (minmax regret) assembly line worker assignment and balancing problem Journal Article COMPUTERS & OPERATIONS RESEARCH, 93 , pp. 27-40, 2018, ISSN: 0305-0548. @article{ISI:000427339800003, title = {The robust (minmax regret) assembly line worker assignment and balancing problem}, author = {Jordi Pereira}, doi = {10.1016/j.cor.2018.01.009}, issn = {0305-0548}, year = {2018}, date = {2018-05-01}, journal = {COMPUTERS & OPERATIONS RESEARCH}, volume = {93}, pages = {27-40}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {Line balancing aims to assign the assembly tasks to the stations that compose the assembly line. A recent body of literature has been devoted to heterogeneity in the assembly process introduced by different workers. In such an environment, task times depend on the worker performing the operation and the problem aims at assigning tasks and workers to stations in order to maximize the throughput of the line. In this work, we consider an interval data version of the assembly line worker assignment and balancing problem (ALWABP) in which it is assumed that lower and upper bounds for the task times are known, and the objective is to find an assignment of tasks and workers to the workstations such that the absolute maximum regret among all of the possible scenarios is minimized. The relationship with other interval data minmax regret (IDMR) problems is investigated, the inapplicability of previous approximation methods is studied, regret evaluation is considered, and exact and heuristic solution methods are proposed and analyzed. The results of the proposed methods are compared in a computational experiment, showing the applicability of the method and the theoretical results to solve the problem under study. Additionally, these results are not only applicable to the problem in hand, but also to a more general class of problems. (C) 2018 Elsevier Ltd. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Line balancing aims to assign the assembly tasks to the stations that compose the assembly line. A recent body of literature has been devoted to heterogeneity in the assembly process introduced by different workers. In such an environment, task times depend on the worker performing the operation and the problem aims at assigning tasks and workers to stations in order to maximize the throughput of the line. In this work, we consider an interval data version of the assembly line worker assignment and balancing problem (ALWABP) in which it is assumed that lower and upper bounds for the task times are known, and the objective is to find an assignment of tasks and workers to the workstations such that the absolute maximum regret among all of the possible scenarios is minimized. The relationship with other interval data minmax regret (IDMR) problems is investigated, the inapplicability of previous approximation methods is studied, regret evaluation is considered, and exact and heuristic solution methods are proposed and analyzed. The results of the proposed methods are compared in a computational experiment, showing the applicability of the method and the theoretical results to solve the problem under study. Additionally, these results are not only applicable to the problem in hand, but also to a more general class of problems. (C) 2018 Elsevier Ltd. All rights reserved. |
Bozkurt, D; Rondanelli, R; í, Mar J C; Garreaud, R Foehn Event Triggered by an Atmospheric River Underlies Record-Setting Temperature Along Continental Antarctica Journal Article Journal of Geophysical Research: Atmospheres, 123 (8), pp. 3871–3892, 2018. @article{Bozkurt2018, title = {Foehn Event Triggered by an Atmospheric River Underlies Record-Setting Temperature Along Continental Antarctica}, author = {D Bozkurt and R Rondanelli and Mar J C \'{i} and R Garreaud}, url = {https://doi.org/10.1002/2017jd027796}, doi = {10.1002/2017jd027796}, year = {2018}, date = {2018-04-01}, journal = {Journal of Geophysical Research: Atmospheres}, volume = {123}, number = {8}, pages = {3871--3892}, publisher = {American Geophysical Union (AGU)}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Rojas-Nunez, J; Gonzalez, R I; Bringa, E M; Allende, S; Sepúlveda, P; Arancibia-Miranda, N; Baltazar, S E Toward Controlled Morphology of FeCu Nanoparticles: Cu Concentration and Size Effects Journal Article Journal of Physical Chemistry C, 122 (15), 2018, ISSN: 19327455. @article{rojas-nunez_toward_2018, title = {Toward Controlled Morphology of FeCu Nanoparticles: Cu Concentration and Size Effects}, author = {J Rojas-Nunez and R I Gonzalez and E M Bringa and S Allende and P Sep\'{u}lveda and N Arancibia-Miranda and S E Baltazar}, doi = {10.1021/acs.jpcc.7b11556}, issn = {19327455}, year = {2018}, date = {2018-01-01}, journal = {Journal of Physical Chemistry C}, volume = {122}, number = {15}, abstract = {© 2018 American Chemical Society. Bimetallic nanoparticles (NPs) can be tailored by varying the concentration of their constituent elements, resulting in novel structures and/or configurations, leading to interesting electronic, mechanical, and chemical properties. In this paper, by means of molecular dynamics calculations, we study the morphology of bimetallic FeCu NPs as a function of the Cu concentration. Our results evidence a core-shell (CS) structure for low Cu concentrations and a Janus (JN)-like morphology for high Cu content. Structural and energy characterizations were performed to determine the atomic-scale behavior of the NPs. Using a continuous model to describe immiscible components, we obtain a stability transition curve between CS and JN-like structures for several NP sizes and concentrations. Results from both methods are compared with experimental data obtained for NPs with low and high Cu content, evidencing a good agreement among the three approaches.}, keywords = {}, pubstate = {published}, tppubtype = {article} } © 2018 American Chemical Society. Bimetallic nanoparticles (NPs) can be tailored by varying the concentration of their constituent elements, resulting in novel structures and/or configurations, leading to interesting electronic, mechanical, and chemical properties. In this paper, by means of molecular dynamics calculations, we study the morphology of bimetallic FeCu NPs as a function of the Cu concentration. Our results evidence a core-shell (CS) structure for low Cu concentrations and a Janus (JN)-like morphology for high Cu content. Structural and energy characterizations were performed to determine the atomic-scale behavior of the NPs. Using a continuous model to describe immiscible components, we obtain a stability transition curve between CS and JN-like structures for several NP sizes and concentrations. Results from both methods are compared with experimental data obtained for NPs with low and high Cu content, evidencing a good agreement among the three approaches. |
Córdoba, Andrés The Effects of the Interplay between Motor and Brownian Forces on the Rheology of Active Gels Journal Article Journal of Physical Chemistry C, pp. 11, 2018. @article{cordoba_effects_2018, title = {The Effects of the Interplay between Motor and Brownian Forces on the Rheology of Active Gels}, author = {Andr\'{e}s C\'{o}rdoba}, doi = {10.1021/acs.jpcb.8b00238}, year = {2018}, date = {2018-01-01}, journal = {Journal of Physical Chemistry C}, pages = {11}, abstract = {Active gels perform key mechanical roles inside the cell, such as cell division, motion, and force sensing. The unique mechanical properties required to perform such functions arise from the interactions between molecular motors and semiflexible polymeric filaments. Molecular motors can convert the energy released in the hydrolysis of ATP into forces of up to piconewton magnitudes. Moreover, the polymeric filaments that form active gels are flexible enough to respond to Brownian forces but also stiff enough to support the large tensions induced by the motor-generated forces. Brownian forces are expected to have a significant effect especially at motor activities at which stable noncontractile in vitro active gels are prepared for rheological measurements. Here, a microscopic mean-field theory of active gels originally formulated in the limit of motor-dominated dynamics is extended to include Brownian forces. In the model presented here, Brownian forces are included accurately, at real room temperature, even in systems with high motor activity. It is shown that a subtle interplay, or competition, between motor-generated forces and Brownian forces has an important impact on the mass transport and rheological properties of active gels. The model predictions show that at low frequencies the dynamic modulus of active gels is determined mostly by motor protein dynamics. However, Brownian forces significantly increase the breadth of the relaxation spectrum and can affect the shape of the dynamic modulus over a wide frequency range even for ratios of motor to Brownian forces of more than a hundred. Since the ratio between motor and Brownian forces is sensitive to ATP concentration, the results presented here shed some light on how the transient mechanical response of active gels changes with varying ATP concentration.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Active gels perform key mechanical roles inside the cell, such as cell division, motion, and force sensing. The unique mechanical properties required to perform such functions arise from the interactions between molecular motors and semiflexible polymeric filaments. Molecular motors can convert the energy released in the hydrolysis of ATP into forces of up to piconewton magnitudes. Moreover, the polymeric filaments that form active gels are flexible enough to respond to Brownian forces but also stiff enough to support the large tensions induced by the motor-generated forces. Brownian forces are expected to have a significant effect especially at motor activities at which stable noncontractile in vitro active gels are prepared for rheological measurements. Here, a microscopic mean-field theory of active gels originally formulated in the limit of motor-dominated dynamics is extended to include Brownian forces. In the model presented here, Brownian forces are included accurately, at real room temperature, even in systems with high motor activity. It is shown that a subtle interplay, or competition, between motor-generated forces and Brownian forces has an important impact on the mass transport and rheological properties of active gels. The model predictions show that at low frequencies the dynamic modulus of active gels is determined mostly by motor protein dynamics. However, Brownian forces significantly increase the breadth of the relaxation spectrum and can affect the shape of the dynamic modulus over a wide frequency range even for ratios of motor to Brownian forces of more than a hundred. Since the ratio between motor and Brownian forces is sensitive to ATP concentration, the results presented here shed some light on how the transient mechanical response of active gels changes with varying ATP concentration. |
Riquelme, Jorge; Neira, Karinna; Marco, José F; Hermosilla-Ibáñez, Patricio; Venegas-Yazigi, Diego; Orellana, Walter; Ponce, Ingrid; Zagal, José H; Tasca, Federico Transactions, E C S Society, The Electrochemical, 85 (12), pp. 111–121, 2018. @article{riquelme_climbing_2018, title = {Climbing Over the Activity Volcano Correlation By Biomimicking Vitamin B12: A Co Phthalocyanine Pyridine Axial Ligand Coordinated Catalyst for the Reduction of Molecular Oxygen Jorge Riquelme,}, author = {Jorge Riquelme and Karinna Neira and Jos\'{e} F Marco and Patricio Hermosilla-Ib\'{a}\~{n}ez and Diego Venegas-Yazigi and Walter Orellana and Ingrid Ponce and Jos\'{e} H Zagal and Federico Tasca}, doi = {10.1149/08512.0111ecst}, year = {2018}, date = {2018-01-01}, journal = {Transactions, E C S Society, The Electrochemical}, volume = {85}, number = {12}, pages = {111--121}, abstract = {CoN4 macrocyclic complexes like Co phthalocyanines (CoPc) have been extensively studied as electrocatalysts for the ORR but they preferentially promote the 2-e reduction of O2 to give peroxide. In contrast, vitamin B12, a naturally occurring CoN4 macrocyclic molecule alkaline media promotes the 4-electron reduction of O2 to H2O. Vitamin B12 possesses an imidazole axial back ligand and this seems to be the reason for its higher activity and selectivity for the 4-e reduction of O2. To test this hypothesis, we synthesized a CoPc axially coordinated to pyridine anchored to carbon nanotubes (Co-Py-CNT). The Co center is therefore coordinated to 5 nitrogens as in vitamin B12. The modified CoPcPy containing catalytic material was characterized by EPR and XPS spectroscopy. DFT calculations. According to our results the pyridine back ligand increases the Co-O2 binding energy, making it more similar to VitB12, favoring the splitting of the O-O bond. The back ligand then plays a crucial role in modifying Co- O2 binding energy which is a well know reactivity descriptor. A further evidence of this dramatic change in reactivity of CoPc by the presence of the "Py" back ligand is that it moves from the weak binding leg of a volcano correlation to the strong leg of the volcano. This might explain why nature uses a back ligand in cytochrome c to catalyze the ORR.}, keywords = {}, pubstate = {published}, tppubtype = {article} } CoN4 macrocyclic complexes like Co phthalocyanines (CoPc) have been extensively studied as electrocatalysts for the ORR but they preferentially promote the 2-e reduction of O2 to give peroxide. In contrast, vitamin B12, a naturally occurring CoN4 macrocyclic molecule alkaline media promotes the 4-electron reduction of O2 to H2O. Vitamin B12 possesses an imidazole axial back ligand and this seems to be the reason for its higher activity and selectivity for the 4-e reduction of O2. To test this hypothesis, we synthesized a CoPc axially coordinated to pyridine anchored to carbon nanotubes (Co-Py-CNT). The Co center is therefore coordinated to 5 nitrogens as in vitamin B12. The modified CoPcPy containing catalytic material was characterized by EPR and XPS spectroscopy. DFT calculations. According to our results the pyridine back ligand increases the Co-O2 binding energy, making it more similar to VitB12, favoring the splitting of the O-O bond. The back ligand then plays a crucial role in modifying Co- O2 binding energy which is a well know reactivity descriptor. A further evidence of this dramatic change in reactivity of CoPc by the presence of the "Py" back ligand is that it moves from the weak binding leg of a volcano correlation to the strong leg of the volcano. This might explain why nature uses a back ligand in cytochrome c to catalyze the ORR. |
Hart, Andrew; Cortés, María Paz; Latorre, Mauricio; Martinez, Servet Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium Journal Article PLOS ONE, 13 (5), pp. 1–17, 2018. @article{hart_codon_2018, title = {Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium}, author = {Andrew Hart and Mar\'{i}a Paz Cort\'{e}s and Mauricio Latorre and Servet Martinez}, url = {https://doi.org/10.1371/journal.pone.0195869}, doi = {10.1371/journal.pone.0195869}, year = {2018}, date = {2018-01-01}, journal = {PLOS ONE}, volume = {13}, number = {5}, pages = {1--17}, abstract = {The analysis of codon usage bias has been widely used to characterize different communities of microorganisms. In this context, the aim of this work was to study the codon usage bias in a natural consortium of five acidophilic bacteria used for biomining. The codon usage bias of the consortium was contrasted with genes from an alternative collection of acidophilic reference strains and metagenome samples. Results indicate that acidophilic bacteria preferentially have low codon usage bias, consistent with both their capacity to live in a wide range of habitats and their slow growth rate, a characteristic probably acquired independently from their phylogenetic relationships. In addition, the analysis showed significant differences in the unique sets of genes from the autotrophic species of the consortium in relation to other acidophilic organisms, principally in genes which code for proteins involved in metal and oxidative stress resistance. The lower values of codon usage bias obtained in this unique set of genes suggest higher transcriptional adaptation to living in extreme conditions, which was probably acquired as a measure for resisting the elevated metal conditions present in the mine.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The analysis of codon usage bias has been widely used to characterize different communities of microorganisms. In this context, the aim of this work was to study the codon usage bias in a natural consortium of five acidophilic bacteria used for biomining. The codon usage bias of the consortium was contrasted with genes from an alternative collection of acidophilic reference strains and metagenome samples. Results indicate that acidophilic bacteria preferentially have low codon usage bias, consistent with both their capacity to live in a wide range of habitats and their slow growth rate, a characteristic probably acquired independently from their phylogenetic relationships. In addition, the analysis showed significant differences in the unique sets of genes from the autotrophic species of the consortium in relation to other acidophilic organisms, principally in genes which code for proteins involved in metal and oxidative stress resistance. The lower values of codon usage bias obtained in this unique set of genes suggest higher transcriptional adaptation to living in extreme conditions, which was probably acquired as a measure for resisting the elevated metal conditions present in the mine. |
Slater, Paula G; Gutierrez-Maldonado, Sebastian E; Gysling, Katia; Lagos, Carlos F Molecular modeling of structures and interaction of human corticotropin-releasing factor (CRF) binding protein and CRF Type-2 receptor Journal Article Frontiers in Endocrinology, 9 (FEB), pp. 1–14, 2018, ISSN: 16642392. @article{slater_molecular_2018, title = {Molecular modeling of structures and interaction of human corticotropin-releasing factor (CRF) binding protein and CRF Type-2 receptor}, author = {Paula G Slater and Sebastian E Gutierrez-Maldonado and Katia Gysling and Carlos F Lagos}, doi = {10.3389/fendo.2018.00043}, issn = {16642392}, year = {2018}, date = {2018-01-01}, journal = {Frontiers in Endocrinology}, volume = {9}, number = {FEB}, pages = {1--14}, abstract = {The corticotropin-releasing factor (CRF) system is a key mediator of the stress response and addictive behavior. The CRF system includes four peptides: The CRF system includes four peptides: CRF, urocortins I-III, CRF binding protein (CRF-BP) that binds CRF with high affinity, and two class B G-protein coupled receptors CRF1R and CRF2R. CRF-BP is a secreted protein without significant sequence homology to CRF receptors or to any other known class of protein. Recently, it has been described a potentiation role of CRF-BP over CRF signaling through CRF2R in addictive-related neuronal plasticity and behavior. In addition, it has been described that CRF-BP is capable to physically interact specifically with the α isoform of CRF2R and acts like an escort protein increasing the amount of the receptor in the plasma membrane. At present, there are no available structures for CRF-BP or for full-length CRFR. Knowing and studying the structure of these proteins could be beneficial in order to characterize the CRF-BP/CRF2αR interaction. In this work, we report the modeling of CRF-BP and of full-length CRF2αR and CRF2βR based on the recently solved crystal structures of the transmembrane domains of the human glucagon receptor and human CRF1R, in addition with the resolved N-terminal extracellular domain of CRFRs. These models were further studied using molecular dynamics simulations and protein-protein docking. The results predicted a higher possibility of interaction of CRF-BP with CRF2αR than CRF2βR and yielded the possible residues conforming the interacting interface. Thus, the present study provides a framework for further investigation of the CRF-BP/CRF2αR interaction.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The corticotropin-releasing factor (CRF) system is a key mediator of the stress response and addictive behavior. The CRF system includes four peptides: The CRF system includes four peptides: CRF, urocortins I-III, CRF binding protein (CRF-BP) that binds CRF with high affinity, and two class B G-protein coupled receptors CRF1R and CRF2R. CRF-BP is a secreted protein without significant sequence homology to CRF receptors or to any other known class of protein. Recently, it has been described a potentiation role of CRF-BP over CRF signaling through CRF2R in addictive-related neuronal plasticity and behavior. In addition, it has been described that CRF-BP is capable to physically interact specifically with the α isoform of CRF2R and acts like an escort protein increasing the amount of the receptor in the plasma membrane. At present, there are no available structures for CRF-BP or for full-length CRFR. Knowing and studying the structure of these proteins could be beneficial in order to characterize the CRF-BP/CRF2αR interaction. In this work, we report the modeling of CRF-BP and of full-length CRF2αR and CRF2βR based on the recently solved crystal structures of the transmembrane domains of the human glucagon receptor and human CRF1R, in addition with the resolved N-terminal extracellular domain of CRFRs. These models were further studied using molecular dynamics simulations and protein-protein docking. The results predicted a higher possibility of interaction of CRF-BP with CRF2αR than CRF2βR and yielded the possible residues conforming the interacting interface. Thus, the present study provides a framework for further investigation of the CRF-BP/CRF2αR interaction. |
Suzuki, Kosuke; Aravena, Daniel; Minato, Takuo; Ruiz, Eliseo; Yamaguchi, Kazuya; Mizuno, Noritaka Effect of Heteroatoms on Field-Induced Slow Magnetic Relaxation of Mononuclear FeIII (S = 5/2) Ions within Polyoxometalates Journal Article Inorganic Chemistry, 3 , pp. 2–4, 2018. @article{suzuki_effect_2018, title = {Effect of Heteroatoms on Field-Induced Slow Magnetic Relaxation of Mononuclear FeIII (S = 5/2) Ions within Polyoxometalates}, author = {Kosuke Suzuki and Daniel Aravena and Takuo Minato and Eliseo Ruiz and Kazuya Yamaguchi and Noritaka Mizuno}, doi = {10.1021/acs.inorgchem.8b00644}, year = {2018}, date = {2018-01-01}, journal = {Inorganic Chemistry}, volume = {3}, pages = {2--4}, abstract = {In this paper, the synthesis and magnetic properties of mononuclear FeIII-containing polyoxometalates (POMs) with differ- ent types of heteroatoms, TBA7H10[(A-α-XW9O34)2Fe] (IIX}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this paper, the synthesis and magnetic properties of mononuclear FeIII-containing polyoxometalates (POMs) with differ- ent types of heteroatoms, TBA7H10[(A-α-XW9O34)2Fe] (IIX |
Santana, Ricardo De; Fuentealba, Pablo; Maia, Lauro; Paredes-Garcia, Veronica; Aravena, Daniel; Venegas-Yazigi, Diego; Manzur, Jorge; Spodine, Evgenia Solid state photoluminescence studies of [EuLnH2(NO3)3](Ħ2O)x macrocyclic complexes with Schiff base ligands Journal Article Journal of Luminescence, 2018, ISSN: 0022-2313. @article{de_santana_solid_2018, title = {Solid state photoluminescence studies of [EuLnH2(NO3)3]({H}2O)x macrocyclic complexes with Schiff base ligands}, author = {Ricardo De Santana and Pablo Fuentealba and Lauro Maia and Veronica Paredes-Garcia and Daniel Aravena and Diego Venegas-Yazigi and Jorge Manzur and Evgenia Spodine}, url = {https://doi.org/10.1016/j.jlumin.2018.06.022}, doi = {10.1016/j.jlumin.2018.06.022}, issn = {0022-2313}, year = {2018}, date = {2018-01-01}, journal = {Journal of Luminescence}, abstract = {Three EuIII macrocyclic complexes [EuLnH2(NO3)3](H2O)x based on the ligands derived from 2-hydroxy-5- methyl-1,3-benzenedicarbaldehyde and three different amines: o-phenylenediamine, Eu-OPDA; ethylenedia- mine, Eu-EDA; and 1,3-diaminopropane, Eu-DAP have been synthesized via a metal template reaction. Eu- EDA and Eu-DAP showed metal based emission; for the Eu-OPDA complex these luminescent properties were not observed. From the photoluminescence emission measurements from ∼13 to 300 K, the R/O = I (5D0 → 7F2)/I (5D0 → 7F1) ratio, together with two intensity parameters ($\Omega$2 and $\Omega$4), radiative lifetimes (τR) and branching ratios (β0 J′) were calculated based on the Judd-Ofelt theory, for Eu-EDA and Eu-DAP. While the behavior of these parameters for the Eu-DAP complex is temperature dependent, these remain constant for Eu- EDA. The temperature dependence observed for the Eu-DAP complex indicates that for temperatures below 120 K, the local symmetry of the EuIII center is modified, as compared to the environment of the same metal center at room temperature.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Three EuIII macrocyclic complexes [EuLnH2(NO3)3](H2O)x based on the ligands derived from 2-hydroxy-5- methyl-1,3-benzenedicarbaldehyde and three different amines: o-phenylenediamine, Eu-OPDA; ethylenedia- mine, Eu-EDA; and 1,3-diaminopropane, Eu-DAP have been synthesized via a metal template reaction. Eu- EDA and Eu-DAP showed metal based emission; for the Eu-OPDA complex these luminescent properties were not observed. From the photoluminescence emission measurements from ∼13 to 300 K, the R/O = I (5D0 → 7F2)/I (5D0 → 7F1) ratio, together with two intensity parameters ($Ømega$2 and $Ømega$4), radiative lifetimes (τR) and branching ratios (β0 J′) were calculated based on the Judd-Ofelt theory, for Eu-EDA and Eu-DAP. While the behavior of these parameters for the Eu-DAP complex is temperature dependent, these remain constant for Eu- EDA. The temperature dependence observed for the Eu-DAP complex indicates that for temperatures below 120 K, the local symmetry of the EuIII center is modified, as compared to the environment of the same metal center at room temperature. |
Xiang, Yuan; Camarada, María Belén; Wen, Yangping; Wu, Hao; Chen, Jinyin; Li, Mingfang; Liao, Xiaoning Simple voltammetric analyses of ochratoxin A in food samples using highly-stable and anti-fouling black phosphorene nanosensor Journal Article Electrochimica Acta, 282 , pp. 490–498, 2018, ISSN: 00134686. @article{xiang_simple_2018, title = {Simple voltammetric analyses of ochratoxin A in food samples using highly-stable and anti-fouling black phosphorene nanosensor}, author = {Yuan Xiang and Mar\'{i}a Bel\'{e}n Camarada and Yangping Wen and Hao Wu and Jinyin Chen and Mingfang Li and Xiaoning Liao}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0013468618313434}, doi = {10.1016/j.electacta.2018.06.055}, issn = {00134686}, year = {2018}, date = {2018-01-01}, journal = {Electrochimica Acta}, volume = {282}, pages = {490--498}, abstract = {There are few reports on the electrochemical detection of ochratoxin A (OTA) using chemically modified electrode owing to the OTA poor electrochemical activity and strong fouling effect towards electrode surface. In this study, a novel nanosensor based on two-dimensional (2D) layered black phosphorene (BP) was successfully developed for the simple voltammetric detection of OTA in grape juice and red wine samples. The BP modified nanosensor showed a good linear electrochemical response towards OTA in a concentration range of 0.3\textendash10 μg/mL with a detection limit of 0.18 μg/mL (S/N = 3) under the optimal conditions. A mechanism for the electrocatalytic oxidation of OTA was proposed and verified by density functional theory calculations that the oxidation of OTA is an irreversible electrochemical response with an adsorption-controlled process, and the nitrogen atom of the amide is oxidized to N+O− with two protons and two electrons. The proposed electrochemical sensor demonstrated good electrochemical stability, superior anti-fouling property and excellent sensitivity towards OTA detection. A satisfactory practicability with recoveries between 98.8% and 103.3% was obtained in real samples determination. This work puts forward a new sensing platform based on the two-dimensional layered graphene-like nanosensor for the electrochemical determination of mycotoxins in edible agricultural food.}, keywords = {}, pubstate = {published}, tppubtype = {article} } There are few reports on the electrochemical detection of ochratoxin A (OTA) using chemically modified electrode owing to the OTA poor electrochemical activity and strong fouling effect towards electrode surface. In this study, a novel nanosensor based on two-dimensional (2D) layered black phosphorene (BP) was successfully developed for the simple voltammetric detection of OTA in grape juice and red wine samples. The BP modified nanosensor showed a good linear electrochemical response towards OTA in a concentration range of 0.3–10 μg/mL with a detection limit of 0.18 μg/mL (S/N = 3) under the optimal conditions. A mechanism for the electrocatalytic oxidation of OTA was proposed and verified by density functional theory calculations that the oxidation of OTA is an irreversible electrochemical response with an adsorption-controlled process, and the nitrogen atom of the amide is oxidized to N+O− with two protons and two electrons. The proposed electrochemical sensor demonstrated good electrochemical stability, superior anti-fouling property and excellent sensitivity towards OTA detection. A satisfactory practicability with recoveries between 98.8% and 103.3% was obtained in real samples determination. This work puts forward a new sensing platform based on the two-dimensional layered graphene-like nanosensor for the electrochemical determination of mycotoxins in edible agricultural food. |
Contreras, Antonio V; Llanes, Antonio; Pérez-Bernabeu, Alberto; Navarro, Sergio; Pérez-Sánchez, Horacio; López-Espín, Jose J; Cecilia, José M ENMX: An elastic network model to predict the FOREX market evolution Journal Article Simulation Modelling Practice and Theory, 86 (April), pp. 1–10, 2018, ISSN: 1569190X. @article{contreras_enmx:_2018, title = {ENMX: An elastic network model to predict the FOREX market evolution}, author = {Antonio V Contreras and Antonio Llanes and Alberto P\'{e}rez-Bernabeu and Sergio Navarro and Horacio P\'{e}rez-S\'{a}nchez and Jose J L\'{o}pez-Esp\'{i}n and Jos\'{e} M Cecilia}, url = {https://doi.org/10.1016/j.simpat.2018.04.008}, doi = {10.1016/j.simpat.2018.04.008}, issn = {1569190X}, year = {2018}, date = {2018-01-01}, journal = {Simulation Modelling Practice and Theory}, volume = {86}, number = {April}, pages = {1--10}, abstract = {The foreign exchange (FOREX) market is a financial market in which participants, such as international banks, companies or private investors, can both invest in and speculate on exchange rates. This market is considered one of the largest financial markets in the world in terms of trading volume. Indeed, the just-in-time price prediction for a currency pair exchange rate (e.g. EUR/USD) provides valuable information for companies and investors as they can take different actions to improve their business. This paper introduces a new algorithm, inspired by the behaviour of macromolecules in dissolution, to model the evolution of the FOREX market, called the ENMX (elastic network model for FOREX market) algorithm. This algorithm allows the system to escape from a potential local minimum, so it can reproduce the unstable nature of the FOREX market, allowing the simulation to get away from equilibrium. ENMX introduces several novelties in the simulation of the FOREX market. First, ENMX enables the user to simulate the market evolution of up to 21 currency pairs, connected, and thus emulating behaviour of the real-world FOREX market. Second, the interaction between investors and each particular quotation, which may introduce slight deviations from the quotation prices, is represented by a random movement. We analyse different probability distributions like Gaussian and Pseudo-Voigt, the latter showing better behaviour distributions, to model the variations in quotation prices. Finally, the ENMX algorithm is also compared to traditional econometric approaches such as the VAR model and a driftless random walk, using a classical statistical and a profitability measure. The results show that the ENMX outperforms both models in terms of quality by a wide margin.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The foreign exchange (FOREX) market is a financial market in which participants, such as international banks, companies or private investors, can both invest in and speculate on exchange rates. This market is considered one of the largest financial markets in the world in terms of trading volume. Indeed, the just-in-time price prediction for a currency pair exchange rate (e.g. EUR/USD) provides valuable information for companies and investors as they can take different actions to improve their business. This paper introduces a new algorithm, inspired by the behaviour of macromolecules in dissolution, to model the evolution of the FOREX market, called the ENMX (elastic network model for FOREX market) algorithm. This algorithm allows the system to escape from a potential local minimum, so it can reproduce the unstable nature of the FOREX market, allowing the simulation to get away from equilibrium. ENMX introduces several novelties in the simulation of the FOREX market. First, ENMX enables the user to simulate the market evolution of up to 21 currency pairs, connected, and thus emulating behaviour of the real-world FOREX market. Second, the interaction between investors and each particular quotation, which may introduce slight deviations from the quotation prices, is represented by a random movement. We analyse different probability distributions like Gaussian and Pseudo-Voigt, the latter showing better behaviour distributions, to model the variations in quotation prices. Finally, the ENMX algorithm is also compared to traditional econometric approaches such as the VAR model and a driftless random walk, using a classical statistical and a profitability measure. The results show that the ENMX outperforms both models in terms of quality by a wide margin. |
Moreno, Felipe; Davis, Sergio; Loyola, Claudia; Peralta, Joaquín Ordered metastable states in the Potts model and their connection with the superheated solid state Journal Article Physica A: Statistical Mechanics and its Applications, 509 , pp. 361 – 368, 2018, ISSN: 0378-4371. @article{moreno_ordered_2018, title = {Ordered metastable states in the Potts model and their connection with the superheated solid state}, author = {Felipe Moreno and Sergio Davis and Claudia Loyola and Joaqu\'{i}n Peralta}, url = {http://www.sciencedirect.com/science/article/pii/S0378437118307301}, doi = {https://doi.org/10.1016/j.physa.2018.06.006}, issn = {0378-4371}, year = {2018}, date = {2018-01-01}, journal = {Physica A: Statistical Mechanics and its Applications}, volume = {509}, pages = {361 -- 368}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ríos-González, J A; Menéndez-Proupin, E; Peña, J L Theoretical study of bismuth-doped CdTe Journal Article Journal of Physics: Conference Series, 1043 (1), pp. 012044, 2018. @article{1742-6596-1043-1-012044, title = {Theoretical study of bismuth-doped CdTe}, author = {J A R\'{i}os-Gonz\'{a}lez and E Men\'{e}ndez-Proupin and J L Pe\~{n}a}, url = {http://stacks.iop.org/1742-6596/1043/i=1/a=012044}, year = {2018}, date = {2018-01-01}, journal = {Journal of Physics: Conference Series}, volume = {1043}, number = {1}, pages = {012044}, abstract = {The electronic structure and thermodynamic properties of bismuth impurities in cadmium telluride (CdTe) are studied by means density functional theory calculations. The exchange and correlation are treated using the hybrid functional HSE, where the range-separation parameter is tuned to fit the CdTe band gap. The spin-orbit coupling is included in the calculations, showing a strong effect on the Bi-related energy levels. The band diagram and the formation energies are obtained for substitutional and interstitial configurations. It is shown that simple substitutional impurities can generate in-gap bands, which can act as intermediate levels in two-photon absorption and can be appropriate for intermediate-band solar cells.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The electronic structure and thermodynamic properties of bismuth impurities in cadmium telluride (CdTe) are studied by means density functional theory calculations. The exchange and correlation are treated using the hybrid functional HSE, where the range-separation parameter is tuned to fit the CdTe band gap. The spin-orbit coupling is included in the calculations, showing a strong effect on the Bi-related energy levels. The band diagram and the formation energies are obtained for substitutional and interstitial configurations. It is shown that simple substitutional impurities can generate in-gap bands, which can act as intermediate levels in two-photon absorption and can be appropriate for intermediate-band solar cells. |
Casanova-Páez, M; Menéndez-Proupin, E Density functional theory study of defects in cadmium telluride: a PBC and QM/MM comparison Journal Article Journal of Physics: Conference Series, 1043 (1), pp. 012043, 2018. @article{1742-6596-1043-1-012043, title = {Density functional theory study of defects in cadmium telluride: a PBC and QM/MM comparison}, author = {M Casanova-P\'{a}ez and E Men\'{e}ndez-Proupin}, url = {http://stacks.iop.org/1742-6596/1043/i=1/a=012043}, year = {2018}, date = {2018-01-01}, journal = {Journal of Physics: Conference Series}, volume = {1043}, number = {1}, pages = {012043}, abstract = {Ab initio calculations, in the framework of density functional theory (DFT), are employed to determine the formation energies of tellurium vacancy (VTe) for different ionized states. We performed a periodic boundary conditions (PBC) calculation, applying quasiparticle corrections and establishing the thermodynamic transition level. In addition, we have also used the quantum mechanics/molecular mechanics (QM/MM) approach in order to check its capability predicting formation energies, finding similar results compared to the previous supercell method.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Ab initio calculations, in the framework of density functional theory (DFT), are employed to determine the formation energies of tellurium vacancy (VTe) for different ionized states. We performed a periodic boundary conditions (PBC) calculation, applying quasiparticle corrections and establishing the thermodynamic transition level. In addition, we have also used the quantum mechanics/molecular mechanics (QM/MM) approach in order to check its capability predicting formation energies, finding similar results compared to the previous supercell method. |
Recent Activities
- 3rd Engineering and Sciences Festival at Universidad de Chile
- The NLHPC invites you to the Workshop: Programming GPUs with CUDA
- GPUs Programing with CUDA Workshop
- II Workshop on Technology Transfer
- Charla Computación de Alto Rendimiento en Ingeniería Computacional: Aplicaciones Industriales
- Curso VI-HPS. Análisis de Rendimiento de Aplicaciones Paralelas
