Publications that acknowledge the role of the NLHPC in their research
2020 |
Cáceres-Soto, M; Sepúlveda, H H; Muñoz-Mellado, K; Artal, O Comparison of QuikSCAT, WRF and buoy ocean surface wind data off Valparaiso Bay, Chile Journal Article Journal of Marine Systems, 203 , pp. 103263, 2020. @article{CceresSoto2020, title = {Comparison of QuikSCAT, WRF and buoy ocean surface wind data off Valparaiso Bay, Chile}, author = {M C\'{a}ceres-Soto and H H Sep\'{u}lveda and K Mu\~{n}oz-Mellado and O Artal}, url = {https://doi.org/10.1016/j.jmarsys.2019.103263}, doi = {10.1016/j.jmarsys.2019.103263}, year = {2020}, date = {2020-01-01}, journal = {Journal of Marine Systems}, volume = {203}, pages = {103263}, publisher = {Elsevier BV}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
í, J A R; Mis-Fernández, R; Camacho-Espinosa, E; Riech, I; Menéndez-Proupin, E; Flores, M A; Orellana, W; Peña, J L Inducing a level inside of CdTe bandgap doping with Sn using a co-sublimation technique by CSS Journal Article Materials Science in Semiconductor Processing, 107 , pp. 104836, 2020. @article{RosGonzlez2020, title = {Inducing a level inside of CdTe bandgap doping with Sn using a co-sublimation technique by CSS}, author = {J A R \'{i} and R Mis-Fern\'{a}ndez and E Camacho-Espinosa and I Riech and E Men\'{e}ndez-Proupin and M A Flores and W Orellana and J L Pe\~{n}a}, url = {https://doi.org/10.1016/j.mssp.2019.104836}, doi = {10.1016/j.mssp.2019.104836}, year = {2020}, date = {2020-01-01}, journal = {Materials Science in Semiconductor Processing}, volume = {107}, pages = {104836}, publisher = {Elsevier BV}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2019 |
González, Juan; González, Gabriel; Aránguiz, Rafael; Melgar, Diego; Zamora, Natalia; Shrivastava, Mahesh N; Das, Ranjit; Catalán, Patricio A; Cienfuegos, Rodrigo A hybrid deterministic and stochastic approach for tsunami hazard assessment in Iquique, Chile Journal Article Natural Hazards, 2019, ISSN: 1573-0840. @article{Gonz\'{a}lez2019b, title = {A hybrid deterministic and stochastic approach for tsunami hazard assessment in Iquique, Chile}, author = {Juan Gonz\'{a}lez and Gabriel Gonz\'{a}lez and Rafael Ar\'{a}nguiz and Diego Melgar and Natalia Zamora and Mahesh N Shrivastava and Ranjit Das and Patricio A Catal\'{a}n and Rodrigo Cienfuegos}, url = {https://doi.org/10.1007/s11069-019-03809-8}, doi = {10.1007/s11069-019-03809-8}, issn = {1573-0840}, year = {2019}, date = {2019-10-08}, journal = {Natural Hazards}, abstract = {The southern Peru and northern Chile coastal region is an active subduction zone that contains one of the most significant seismic gaps in the eastern Pacific basin 24S. Although the gap was partially filled by the 2014 Mw 8.1 Iquique earthquake, there is still a high seismogenic potential to release a Mw9 earthquake in the near future; therefore, all the near-field coastal cities in the region face a latent tsunami threat. In this article, we propose a hybrid deterministic--stochastic multi-scenario approach to assess the current tsunami hazard level in the city of Iquique, an important commercial and industrial center of northern Chile that is home to 184,000 inhabitants. In our approach, we defined 400 stochastic, 10 deterministic and 10 homogeneous tsunamigenic earthquake scenarios, covering the entire area of the seismic gap. Based on the regional distribution of gravity anomalies and published interseismic coupling distributions, we interpreted the occurrence of four major asperities in the subduction interface of the seismic gap. The asperity pattern was used to construct a group of deterministic slip-deficit earthquake sources with seismic magnitudes ranging between Mw 8.4 and Mw 8.9. Additionally, we constructed 10 homogeneous slip scenarios to generate an inundation baseline for the tsunami hazard. Subsequently, following a stochastic scheme, we implemented a Karhunen--Lo\'{e}ve expansion to generate 400 stochastic earthquake scenarios within the same magnitude range as the deterministic slip-deficit sources. All sources were used as earthquake scenarios to simulate the tsunami propagation and inundation by means of a non-hydrostatic model (Neowave 2D) with a classical nesting scheme for the city of Iquique. We obtained high-resolution data for flow depth, coastal surface currents and sea level elevation. The results suggest that the peak slip location and shelf resonance play an important role in the calculated coastal flow depths. The analysis of the entire set of simulated stochastic earthquake scenarios indicates that the worst-case scenario for Iquique is a Mw 8.9 earthquake. This scenario presented a tsunami arrival time of 12 min, which is critical for the evacuation process. In addition, the maximum wave height and tsunami flow depth were found to be 10 m and 24 m, respectively. The observed coastal resonance processes exhibit at least three destructive tsunami wave trains. Based on historical and instrumental catalog statistics, the recurrence time of the credible worst-case earthquake scenario for Iquique (Mw 8.9) is 395 years, with a probability of occurrence of 11.86% in the next 50 years.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The southern Peru and northern Chile coastal region is an active subduction zone that contains one of the most significant seismic gaps in the eastern Pacific basin 24S. Although the gap was partially filled by the 2014 Mw 8.1 Iquique earthquake, there is still a high seismogenic potential to release a Mw9 earthquake in the near future; therefore, all the near-field coastal cities in the region face a latent tsunami threat. In this article, we propose a hybrid deterministic--stochastic multi-scenario approach to assess the current tsunami hazard level in the city of Iquique, an important commercial and industrial center of northern Chile that is home to 184,000 inhabitants. In our approach, we defined 400 stochastic, 10 deterministic and 10 homogeneous tsunamigenic earthquake scenarios, covering the entire area of the seismic gap. Based on the regional distribution of gravity anomalies and published interseismic coupling distributions, we interpreted the occurrence of four major asperities in the subduction interface of the seismic gap. The asperity pattern was used to construct a group of deterministic slip-deficit earthquake sources with seismic magnitudes ranging between Mw 8.4 and Mw 8.9. Additionally, we constructed 10 homogeneous slip scenarios to generate an inundation baseline for the tsunami hazard. Subsequently, following a stochastic scheme, we implemented a Karhunen--Loéve expansion to generate 400 stochastic earthquake scenarios within the same magnitude range as the deterministic slip-deficit sources. All sources were used as earthquake scenarios to simulate the tsunami propagation and inundation by means of a non-hydrostatic model (Neowave 2D) with a classical nesting scheme for the city of Iquique. We obtained high-resolution data for flow depth, coastal surface currents and sea level elevation. The results suggest that the peak slip location and shelf resonance play an important role in the calculated coastal flow depths. The analysis of the entire set of simulated stochastic earthquake scenarios indicates that the worst-case scenario for Iquique is a Mw 8.9 earthquake. This scenario presented a tsunami arrival time of 12 min, which is critical for the evacuation process. In addition, the maximum wave height and tsunami flow depth were found to be 10 m and 24 m, respectively. The observed coastal resonance processes exhibit at least three destructive tsunami wave trains. Based on historical and instrumental catalog statistics, the recurrence time of the credible worst-case earthquake scenario for Iquique (Mw 8.9) is 395 years, with a probability of occurrence of 11.86% in the next 50 years. |
Maulen, Boris; Echeverri, Andrea; Gomez, Tatiana; Fuentealba, Patricio; Cardenas, Carlos Electron Localization Function in Excited States: The Case of the Ultrafast Proton Transfer of the Salicylidene Methylamine Journal Article JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 15 (10), pp. 5532-5542, 2019, ISSN: 1549-9618. @article{ISI:000489678700032, title = {Electron Localization Function in Excited States: The Case of the Ultrafast Proton Transfer of the Salicylidene Methylamine}, author = {Boris Maulen and Andrea Echeverri and Tatiana Gomez and Patricio Fuentealba and Carlos Cardenas}, doi = {10.1021/acs.jctc.9b00691}, issn = {1549-9618}, year = {2019}, date = {2019-10-01}, journal = {JOURNAL OF CHEMICAL THEORY AND COMPUTATION}, volume = {15}, number = {10}, pages = {5532-5542}, abstract = {The physical characterization of the chemical bond in the ground state has been a central theme to theoretical chemistry. Among many techniques, quantum chemical topology (QCT) has emerged as a robust technique to understand the features of the chemical bond and electron organization within molecules. One consolidate tool within QCT is the topological analysis of the electron localization function (ELF). Most research on ELF and chemical bond has focused either on singlet ground states or the first excited triplet. However, most photochemical reactions and photophysical processes occur in excited states with the same spin-symmetry as the ground state. In this work, we develop a proposal on how to compute the ELF in excited states of any symmetry within linear-response time-dependent density functional theory. Then, we study the evolution of the chemical bonds in the ground- and excited-state intramolecular proton transfer (ESIPT) of a prototypal Schiff base (the salicylidene methylamine). We found that the topological analysis of the ELF along reaction paths explains the presence of a barrier for the proton transfer in the ground state and the absence of it in the excited state. Briefly, in the ground state, the cleavage of the O-H bond results in a structure with high electrostatic potential energy due to an excess of electron lone-pairs (3) in the oxygen atom, which explains the barrier. In the excited state, the electronic transition promotes an enhancement of the basicity of nitrogen by allocating three nonbonding electrons in the basin of its lone-pair. This excess of electrons in the N exerts an electrostatic attraction of the proton, which we suggest as the primary driven-force of the barrierless reaction. Because in excited states the molecule can develop more vibrational kinetic energy than in the ground state, we performed an ab initio molecular dynamics of the proton transfer in the excited state and corroborate that our conclusions on the topology of the ELF do not change due to dynamic effects.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The physical characterization of the chemical bond in the ground state has been a central theme to theoretical chemistry. Among many techniques, quantum chemical topology (QCT) has emerged as a robust technique to understand the features of the chemical bond and electron organization within molecules. One consolidate tool within QCT is the topological analysis of the electron localization function (ELF). Most research on ELF and chemical bond has focused either on singlet ground states or the first excited triplet. However, most photochemical reactions and photophysical processes occur in excited states with the same spin-symmetry as the ground state. In this work, we develop a proposal on how to compute the ELF in excited states of any symmetry within linear-response time-dependent density functional theory. Then, we study the evolution of the chemical bonds in the ground- and excited-state intramolecular proton transfer (ESIPT) of a prototypal Schiff base (the salicylidene methylamine). We found that the topological analysis of the ELF along reaction paths explains the presence of a barrier for the proton transfer in the ground state and the absence of it in the excited state. Briefly, in the ground state, the cleavage of the O-H bond results in a structure with high electrostatic potential energy due to an excess of electron lone-pairs (3) in the oxygen atom, which explains the barrier. In the excited state, the electronic transition promotes an enhancement of the basicity of nitrogen by allocating three nonbonding electrons in the basin of its lone-pair. This excess of electrons in the N exerts an electrostatic attraction of the proton, which we suggest as the primary driven-force of the barrierless reaction. Because in excited states the molecule can develop more vibrational kinetic energy than in the ground state, we performed an ab initio molecular dynamics of the proton transfer in the excited state and corroborate that our conclusions on the topology of the ELF do not change due to dynamic effects. |
Caceres, Giovanna; Lopez, Maria E; Cadiz, Maria I; Yoshida, Grazyella M; Jedlicki, Ana; Palma-Vejares, Ricardo; Travisany, Dante; Diaz-Dominguez, Diego; Maass, Alejandro; Lhorente, Jean P; Soto, Jose; Salas, Diego; Yanez, Jose M G3-GENES GENOMES GENETICS, 9 (10), pp. 3213-3223, 2019, ISSN: 2160-1836. @article{ISI:000490151100014, title = {Fine Mapping Using Whole-Genome Sequencing Confirms Anti-Mullerian Hormone as a Major Gene for Sex Determination in Farmed Nile Tilapia (Oreochromis niloticus L.)}, author = {Giovanna Caceres and Maria E Lopez and Maria I Cadiz and Grazyella M Yoshida and Ana Jedlicki and Ricardo Palma-Vejares and Dante Travisany and Diego Diaz-Dominguez and Alejandro Maass and Jean P Lhorente and Jose Soto and Diego Salas and Jose M Yanez}, doi = {10.1534/g3.119.400297}, issn = {2160-1836}, year = {2019}, date = {2019-10-01}, journal = {G3-GENES GENOMES GENETICS}, volume = {9}, number = {10}, pages = {3213-3223}, abstract = {Nile tilapia (Oreochromis niloticus) is one of the most cultivated and economically important species in world aquaculture. Intensive production promotes the use of monosex animals, due to an important dimorphism that favors male growth. Currently, the main mechanism to obtain all-male populations is the use of hormones in feeding during larval and fry phases. Identifying genomic regions associated with sex determination in Nile tilapia is a research topic of great interest. The objective of this study was to identify genomic variants associated with sex determination in three commercial populations of Nile tilapia. Whole-genome sequencing of 326 individuals was performed, and a total of 2.4 million high-quality bi-allelic single nucleotide polymorphisms (SNPs) were identified after quality control. A genome-wide association study (GWAS) was conducted to identify markers associated with the binary sex trait (males = 1; females = 0). A mixed logistic regression GWAS model was fitted and a genome-wide significant signal comprising 36 SNPs, spanning a genomic region of 536 kb in chromosome 23 was identified. Ten out of these 36 genetic variants intercept the anti-Mullerian (Amh) hormone gene. Other significant SNPs were located in the neighboring Amh gene region. This gene has been strongly associated with sex determination in several vertebrate species, playing an essential role in the differentiation of male and female reproductive tissue in early stages of development. This finding provides useful information to better understand the genetic mechanisms underlying sex determination in Nile tilapia.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Nile tilapia (Oreochromis niloticus) is one of the most cultivated and economically important species in world aquaculture. Intensive production promotes the use of monosex animals, due to an important dimorphism that favors male growth. Currently, the main mechanism to obtain all-male populations is the use of hormones in feeding during larval and fry phases. Identifying genomic regions associated with sex determination in Nile tilapia is a research topic of great interest. The objective of this study was to identify genomic variants associated with sex determination in three commercial populations of Nile tilapia. Whole-genome sequencing of 326 individuals was performed, and a total of 2.4 million high-quality bi-allelic single nucleotide polymorphisms (SNPs) were identified after quality control. A genome-wide association study (GWAS) was conducted to identify markers associated with the binary sex trait (males = 1; females = 0). A mixed logistic regression GWAS model was fitted and a genome-wide significant signal comprising 36 SNPs, spanning a genomic region of 536 kb in chromosome 23 was identified. Ten out of these 36 genetic variants intercept the anti-Mullerian (Amh) hormone gene. Other significant SNPs were located in the neighboring Amh gene region. This gene has been strongly associated with sex determination in several vertebrate species, playing an essential role in the differentiation of male and female reproductive tissue in early stages of development. This finding provides useful information to better understand the genetic mechanisms underlying sex determination in Nile tilapia. |
Huaman-Castilla, Nils Leander; Martinez-Cifuentes, Maximiliano; Camilo, Conrado; Pedreschi, Franco; Mariotti-Celis, Maria; Perez-Correa, Jose Ricardo MOLECULES, 24 (17), 2019. @article{ISI:000488613700125, title = {The Impact of Temperature and Ethanol Concentration on the Global Recovery of Specific Polyphenols in an Integrated HPLE/RP Process on Carmenere Pomace Extracts}, author = {Nils Leander Huaman-Castilla and Maximiliano Martinez-Cifuentes and Conrado Camilo and Franco Pedreschi and Maria Mariotti-Celis and Jose Ricardo Perez-Correa}, doi = {10.3390/molecules24173145}, year = {2019}, date = {2019-09-01}, journal = {MOLECULES}, volume = {24}, number = {17}, abstract = {Sequential extraction and purification stages are required to obtain extracts rich in specific polyphenols. However, both separation processes are often optimized independently and the effect of the integrated process on the global recovery of polyphenols has not been fully elucidated yet. We assessed the impact of hot-pressurized liquid extraction (HPLE) conditions (temperature: 90-150 degrees C; ethanol concentration: 15%-50%) on the global recovery of specific phenolic acids, flavanols, flavonols and stilbenes from Carmenere grape pomace in an integrated HPLE/resin purification (RP) process. HPLE of phenolic acids, flavanols and stilbenes were favored when temperature and ethanol concentration increased, except for chlorogenic acid which showed an increment of its Gibbs free energy of solvation at higher ethanol contents. Ethanol concentration significantly impacted the global yield of the integrated HPLE/RP process. The lower the ethanol content of the HPLE extracts, the higher the recovery of phenolic acids, flavanols and stilbenes after RP, except for flavonols which present more polar functional groups. The best specific recovery conditions were 150 degrees C and ethanol concentrations of 15%, 32.5% and 50% for phenolic acids, flavanols and stilbenes, and flavonols, respectively. At 150 degrees C and 32.5% of ethanol, the extracts presented the highest total polyphenol content and antioxidant capacity. The integrated HPLE/RP process allows a selective separation of specific polyphenols and eliminates the interfering compounds, ensuring the safety of the extracts at all evaluated conditions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Sequential extraction and purification stages are required to obtain extracts rich in specific polyphenols. However, both separation processes are often optimized independently and the effect of the integrated process on the global recovery of polyphenols has not been fully elucidated yet. We assessed the impact of hot-pressurized liquid extraction (HPLE) conditions (temperature: 90-150 degrees C; ethanol concentration: 15%-50%) on the global recovery of specific phenolic acids, flavanols, flavonols and stilbenes from Carmenere grape pomace in an integrated HPLE/resin purification (RP) process. HPLE of phenolic acids, flavanols and stilbenes were favored when temperature and ethanol concentration increased, except for chlorogenic acid which showed an increment of its Gibbs free energy of solvation at higher ethanol contents. Ethanol concentration significantly impacted the global yield of the integrated HPLE/RP process. The lower the ethanol content of the HPLE extracts, the higher the recovery of phenolic acids, flavanols and stilbenes after RP, except for flavonols which present more polar functional groups. The best specific recovery conditions were 150 degrees C and ethanol concentrations of 15%, 32.5% and 50% for phenolic acids, flavanols and stilbenes, and flavonols, respectively. At 150 degrees C and 32.5% of ethanol, the extracts presented the highest total polyphenol content and antioxidant capacity. The integrated HPLE/RP process allows a selective separation of specific polyphenols and eliminates the interfering compounds, ensuring the safety of the extracts at all evaluated conditions. |
Wrighton-Araneda, Kerry; Ruby-Figueroa, René; Estay, Humberto; Cortés-Arriagada, Diego Journal of Molecular Modeling, 25 (9), pp. 291, 2019, ISSN: 0948-5023. @article{Wrighton-Araneda2019, title = {Interaction of H2O with (CuS)n, (Cu2S)n, and (ZnS)n small clusters (nthinspace=thinspace1--4, 6): relation to the aggregation characteristics of metal sulfides at aqueous solutions}, author = {Kerry Wrighton-Araneda and Ren\'{e} Ruby-Figueroa and Humberto Estay and Diego Cort\'{e}s-Arriagada}, url = {https://doi.org/10.1007/s00894-019-4161-x}, doi = {10.1007/s00894-019-4161-x}, issn = {0948-5023}, year = {2019}, date = {2019-08-31}, journal = {Journal of Molecular Modeling}, volume = {25}, number = {9}, pages = {291}, abstract = {The interaction of H2O onto small CuS, Cu2S, and ZnS clusters was theoretically studied by Density Functional Theory computations to get insights into the aggregation characteristics of metal sulfides at aqueous solutions. The results show the charge-controlled interactions with polarized solvent molecules are favored on the ZnS clusters compared with CuS and Cu2S clusters. Moreover, the chemical adsorption of H2O molecules is energetically favored onto ZnS clusters with higher interaction energies of up to 35.4 kcal/mol compared with CuS and Cu2S clusters (up to 31.3 kcal/mol), where the stability of H2O adsorption decreases as the size of the clusters increases. However, thermochemical analysis shows that the adsorption of H2O on copper sulfides is not a spontaneous process at room temperature. Additionally, the electrostatic energy of H2O onto the Cu2S and CuS clusters is lower than that associated with the H2O--H2O interactions, suggesting that copper precipitates prefer to bind between them at early stages of the precipitation process due to an unfavorable solvent-solute interaction. Dispersion forces play a relative key role in the interaction of water on copper sulfides, while for zinc sulfide clusters, the adsorption energy is slightly influenced by dispersion contributions. Accordingly, the aggregation of zinc sulfides in a water environment is expected to be lower compared with copper sulfides, and where the aggregation characteristics are not determined by the binding energy of the sulfides, but of the ability to interact with the solvent molecules. These statements were confirmed by experimental optical microscopy analysis and settling tests during precipitation processes in water. Therefore, this work allows proposing a simple strategy to study the aggregation characteristics of metal sulfides, which turns useful for use in hydrometallurgical applications.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The interaction of H2O onto small CuS, Cu2S, and ZnS clusters was theoretically studied by Density Functional Theory computations to get insights into the aggregation characteristics of metal sulfides at aqueous solutions. The results show the charge-controlled interactions with polarized solvent molecules are favored on the ZnS clusters compared with CuS and Cu2S clusters. Moreover, the chemical adsorption of H2O molecules is energetically favored onto ZnS clusters with higher interaction energies of up to 35.4 kcal/mol compared with CuS and Cu2S clusters (up to 31.3 kcal/mol), where the stability of H2O adsorption decreases as the size of the clusters increases. However, thermochemical analysis shows that the adsorption of H2O on copper sulfides is not a spontaneous process at room temperature. Additionally, the electrostatic energy of H2O onto the Cu2S and CuS clusters is lower than that associated with the H2O--H2O interactions, suggesting that copper precipitates prefer to bind between them at early stages of the precipitation process due to an unfavorable solvent-solute interaction. Dispersion forces play a relative key role in the interaction of water on copper sulfides, while for zinc sulfide clusters, the adsorption energy is slightly influenced by dispersion contributions. Accordingly, the aggregation of zinc sulfides in a water environment is expected to be lower compared with copper sulfides, and where the aggregation characteristics are not determined by the binding energy of the sulfides, but of the ability to interact with the solvent molecules. These statements were confirmed by experimental optical microscopy analysis and settling tests during precipitation processes in water. Therefore, this work allows proposing a simple strategy to study the aggregation characteristics of metal sulfides, which turns useful for use in hydrometallurgical applications. |
Bozkurt, Deniz; Rojas, Maisa; Boisier, Juan Pablo; Rondanelli, Roberto; Garreaud, René; Gallardo, Laura Dynamical downscaling over the complex terrain of southwest South America: present climate conditions and added value analysis Journal Article Climate Dynamics, 2019, ISSN: 1432-0894. @article{Bozkurt2019, title = {Dynamical downscaling over the complex terrain of southwest South America: present climate conditions and added value analysis}, author = {Deniz Bozkurt and Maisa Rojas and Juan Pablo Boisier and Roberto Rondanelli and Ren\'{e} Garreaud and Laura Gallardo}, url = {https://doi.org/10.1007/s00382-019-04959-y}, doi = {10.1007/s00382-019-04959-y}, issn = {1432-0894}, year = {2019}, date = {2019-08-30}, journal = {Climate Dynamics}, abstract = {This study evaluates hindcast simulations performed with a regional climate model (RCM, RegCM4) driven by reanalysis data (ERA-Interim) over the Pacific coast and Andes Cordillera of extratropical South America. A nested domain configuration at (0.44^circ 0.44∘sim∼50 km) and (0.09^circ 0.09∘sim∼10 km) spatial resolutions is used for the simulations. RegCM4 is also driven by a global climate model (GCM, MPI-ESM-MR) on the same domain configuration to asses the added values for temperature and precipitation (historical simulations). Overall, both 10 km hindcast and historical simulation results are promising and exhibit a better representation of near-surface air temperature and precipitation variability compared to the 50 km simulations. High-resolution simulations suppress an overestimation of precipitation over the Andes Cordillera of northern Chile found with the 50 km simulations. The simulated daily temperature and precipitation extreme indices from 10 km hindcast simulation show a closer estimation of the observed fields. A persistent warm bias (sim +,4,circ hbox ∼+4∘C) over the Atacama Desert in 10 km hindcast simulation reveals the complexity in representing land surface and radiative processes over the desert. Difficulties in capturing the temperature trend in northern Chile are notable for both hindcast simulations. Both resolutions exhibit added values for temperature and precipitation over large parts of Chile, in particular, the 10 km resolves the coastal-valley Andes transitions over central Chile. Our results highlight that resolutions coarser than 50 km (e.g., GCMs and reanalysis) miss important climate gradients imposed by complex topography. Given that the highest spatial resolution of the current regional simulations over the South America is about 50 km, higher resolutions are important to improve our understanding of the dynamical processes that determine climate over complex terrain and extreme environments.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This study evaluates hindcast simulations performed with a regional climate model (RCM, RegCM4) driven by reanalysis data (ERA-Interim) over the Pacific coast and Andes Cordillera of extratropical South America. A nested domain configuration at (0.44^circ 0.44∘sim∼50 km) and (0.09^circ 0.09∘sim∼10 km) spatial resolutions is used for the simulations. RegCM4 is also driven by a global climate model (GCM, MPI-ESM-MR) on the same domain configuration to asses the added values for temperature and precipitation (historical simulations). Overall, both 10 km hindcast and historical simulation results are promising and exhibit a better representation of near-surface air temperature and precipitation variability compared to the 50 km simulations. High-resolution simulations suppress an overestimation of precipitation over the Andes Cordillera of northern Chile found with the 50 km simulations. The simulated daily temperature and precipitation extreme indices from 10 km hindcast simulation show a closer estimation of the observed fields. A persistent warm bias (sim +,4,circ hbox ∼+4∘C) over the Atacama Desert in 10 km hindcast simulation reveals the complexity in representing land surface and radiative processes over the desert. Difficulties in capturing the temperature trend in northern Chile are notable for both hindcast simulations. Both resolutions exhibit added values for temperature and precipitation over large parts of Chile, in particular, the 10 km resolves the coastal-valley Andes transitions over central Chile. Our results highlight that resolutions coarser than 50 km (e.g., GCMs and reanalysis) miss important climate gradients imposed by complex topography. Given that the highest spatial resolution of the current regional simulations over the South America is about 50 km, higher resolutions are important to improve our understanding of the dynamical processes that determine climate over complex terrain and extreme environments. |
Herath, Uthpala; Tavadze, Pedram; He, Xu; Bousquet, Eric; Singh, Sobhit; Muñoz, Francisco; Romero, Aldo H PyProcar: A Python library for electronic structure pre/post-processing Journal Article arXiv, 2019. @article{Herath2019, title = {PyProcar: A Python library for electronic structure pre/post-processing}, author = {Uthpala Herath and Pedram Tavadze and Xu He and Eric Bousquet and Sobhit Singh and Francisco Mu\~{n}oz and Aldo H Romero}, url = {http://arxiv.org/abs/1906.11387}, year = {2019}, date = {2019-06-01}, journal = {arXiv}, abstract = {The PyProcar Python package plots the band structure and the Fermi surface as a function of site and/or s,p,d,f - projected wavefunctions obtained for each k-point in the Brillouin zone and band in an electronic structure calculation. This can be performed on top of any electronic structure code, as long as the band and projection information is written in the PROCAR format, as done by the VASP and ABINIT codes. PyProcar can be easily modified to read other formats as well. This package is particularly suitable for understanding atomic effects into the band structure, Fermi surface, spin texture, etc. PyProcar can be conveniently used in a command line mode, where each one of the parameters define a plot property. In the case of Fermi-surfaces, the package is able to plot the surface with colors depending on other properties such as the electron velocity or spin projection. The mesh used to calculate the property does not need to be the same as the one used to obtain the Fermi surface. A file with a specific property evaluated for each k-point in a k-mesh and for each band can be used to project other properties such as electron-phonon mean path, Fermi velocity, electron effective mass, etc. Another existing feature refers to the band unfolding of supercell calculations into predefined unit cells.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The PyProcar Python package plots the band structure and the Fermi surface as a function of site and/or s,p,d,f - projected wavefunctions obtained for each k-point in the Brillouin zone and band in an electronic structure calculation. This can be performed on top of any electronic structure code, as long as the band and projection information is written in the PROCAR format, as done by the VASP and ABINIT codes. PyProcar can be easily modified to read other formats as well. This package is particularly suitable for understanding atomic effects into the band structure, Fermi surface, spin texture, etc. PyProcar can be conveniently used in a command line mode, where each one of the parameters define a plot property. In the case of Fermi-surfaces, the package is able to plot the surface with colors depending on other properties such as the electron velocity or spin projection. The mesh used to calculate the property does not need to be the same as the one used to obtain the Fermi surface. A file with a specific property evaluated for each k-point in a k-mesh and for each band can be used to project other properties such as electron-phonon mean path, Fermi velocity, electron effective mass, etc. Another existing feature refers to the band unfolding of supercell calculations into predefined unit cells. |
Bossy, Mireille; Fontbona, Joaquín; Olivero, Héctor Synchronization of stochastic mean field networks of Hodgkin--Huxley neurons with noisy channels Journal Article Journal of Mathematical Biology, 78 (6), pp. 1771–1820, 2019, ISSN: 1432-1416. @article{Bossy2019, title = {Synchronization of stochastic mean field networks of Hodgkin--Huxley neurons with noisy channels}, author = {Mireille Bossy and Joaqu\'{i}n Fontbona and H\'{e}ctor Olivero}, url = {https://doi.org/10.1007/s00285-019-01326-7}, doi = {10.1007/s00285-019-01326-7}, issn = {1432-1416}, year = {2019}, date = {2019-05-01}, journal = {Journal of Mathematical Biology}, volume = {78}, number = {6}, pages = {1771--1820}, abstract = {In this work we are interested in a mathematical model of the collective behavior of a fully connected network of finitely many neurons, when their number and when time go to infinity. We assume that every neuron follows a stochastic version of the Hodgkin--Huxley model, and that pairs of neurons interact through both electrical and chemical synapses, the global connectivity being of mean field type. When the leak conductance is strictly positive, we prove that if the initial voltages are uniformly bounded and the electrical interaction between neurons is strong enough, then, uniformly in the number of neurons, the whole system synchronizes exponentially fast as time goes to infinity, up to some error controlled by (and vanishing with) the channels noise level. Moreover, we prove that if the random initial condition is exchangeable, on every bounded time interval the propagation of chaos property for this system holds (regardless of the interaction intensities). Combining these results, we deduce that the nonlinear McKean--Vlasov equation describing an infinite network of such neurons concentrates, as time goes to infinity, around the dynamics of a single Hodgkin--Huxley neuron with chemical neurotransmitter channels. Our results are illustrated and complemented with numerical simulations.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this work we are interested in a mathematical model of the collective behavior of a fully connected network of finitely many neurons, when their number and when time go to infinity. We assume that every neuron follows a stochastic version of the Hodgkin--Huxley model, and that pairs of neurons interact through both electrical and chemical synapses, the global connectivity being of mean field type. When the leak conductance is strictly positive, we prove that if the initial voltages are uniformly bounded and the electrical interaction between neurons is strong enough, then, uniformly in the number of neurons, the whole system synchronizes exponentially fast as time goes to infinity, up to some error controlled by (and vanishing with) the channels noise level. Moreover, we prove that if the random initial condition is exchangeable, on every bounded time interval the propagation of chaos property for this system holds (regardless of the interaction intensities). Combining these results, we deduce that the nonlinear McKean--Vlasov equation describing an infinite network of such neurons concentrates, as time goes to infinity, around the dynamics of a single Hodgkin--Huxley neuron with chemical neurotransmitter channels. Our results are illustrated and complemented with numerical simulations. |
Schmidt, Iván; Siddikov, Marat Contribution of digluons to charmonia production Journal Article Journal of Physics G: Nuclear and Particle Physics, 46 (6), pp. 065002, 2019. @article{Schmidt_2019, title = {Contribution of digluons to charmonia production}, author = {Iv\'{a}n Schmidt and Marat Siddikov}, url = {https://doi.org/10.1088%2F1361-6471%2Fab09ab}, doi = {10.1088/1361-6471/ab09ab}, year = {2019}, date = {2019-04-01}, journal = {Journal of Physics G: Nuclear and Particle Physics}, volume = {46}, number = {6}, pages = {065002}, publisher = {IOP Publishing}, abstract = {In this paper we study the contribution of the double parton distributions of gluons to charmonium production. Despite being suppressed in the heavy quark mass limit, numerically, this contribution gives a sizeable correction to the leading order k T factorization result in LHC kinematics due to the enhancement of gluonic densities in the small Bjorken x B limit, and thus presents a complementary mechanism of charmonia production in this kinematics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this paper we study the contribution of the double parton distributions of gluons to charmonium production. Despite being suppressed in the heavy quark mass limit, numerically, this contribution gives a sizeable correction to the leading order k T factorization result in LHC kinematics due to the enhancement of gluonic densities in the small Bjorken x B limit, and thus presents a complementary mechanism of charmonia production in this kinematics. |
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. |
Gallardo-Fuentes, Sebastián; Ormazabal-Toledo, Rodrigo σ-Hole promotes the Concertedness in Nucleophilic Aromatic Substitution reactions of nitroarenes Journal Article New J. Chem., pp. -, 2019. @article{C9NJ01493D, title = {σ-Hole promotes the Concertedness in Nucleophilic Aromatic Substitution reactions of nitroarenes}, author = {Sebasti\'{a}n Gallardo-Fuentes and Rodrigo Ormazabal-Toledo}, url = {http://dx.doi.org/10.1039/C9NJ01493D}, doi = {10.1039/C9NJ01493D}, year = {2019}, date = {2019-01-01}, journal = {New J. Chem.}, pages = {-}, publisher = {The Royal Society of Chemistry}, abstract = {The mechanism of the SNAr reactions between 1-halo-2,4-dinitrobenzenes and amines was revisited by means of DFT calculations. Remarkably and contrary to the traditional text-book perspective, the dehalogenation of 1-X-2,4 -dinitrobenzenes bearing good leaving groups (X=Cl, Br and I) by soft nucleophiles involves a single-step mechanism passing through a barrierless C-X bond cleavage step. Solely the reaction of 1-fluoro-2,4-dinitrobenzene follow the traditional additionelimination pathway. The analysis of the charge transfer patterns along the reaction path for the whole systems studied, suggests that for those nitroarenes exhibiting s-holes the dehalogenation mechanism occurs through a single-step. Nucleophile effects on the reaction rates were also discussed.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The mechanism of the SNAr reactions between 1-halo-2,4-dinitrobenzenes and amines was revisited by means of DFT calculations. Remarkably and contrary to the traditional text-book perspective, the dehalogenation of 1-X-2,4 -dinitrobenzenes bearing good leaving groups (X=Cl, Br and I) by soft nucleophiles involves a single-step mechanism passing through a barrierless C-X bond cleavage step. Solely the reaction of 1-fluoro-2,4-dinitrobenzene follow the traditional additionelimination pathway. The analysis of the charge transfer patterns along the reaction path for the whole systems studied, suggests that for those nitroarenes exhibiting s-holes the dehalogenation mechanism occurs through a single-step. Nucleophile effects on the reaction rates were also discussed. |
Mella, Andy; Cortés-Arriagada, Diego Computational quest of adsorbents based on doped graphene nanosheets for phosgene uptake, and analysis of the co-adsorption phenomena Journal Article Synthetic Metals, 252 , pp. 142 - 150, 2019, ISSN: 0379-6779. @article{MELLA2019142, title = {Computational quest of adsorbents based on doped graphene nanosheets for phosgene uptake, and analysis of the co-adsorption phenomena}, author = {Andy Mella and Diego Cort\'{e}s-Arriagada}, url = {http://www.sciencedirect.com/science/article/pii/S0379677919301316}, doi = {https://doi.org/10.1016/j.synthmet.2019.04.020}, issn = {0379-6779}, year = {2019}, date = {2019-01-01}, journal = {Synthetic Metals}, volume = {252}, pages = {142 - 150}, abstract = {A density functional theory study was performed to analyse the interaction of COCl2 onto A-doped graphene nanosheets (AG, where A: Al, Si, Ti, Cr, Mn, Fe). Adsorption configurations, adsorption energies, electronic properties, and the interaction in a co-adsorption regime were characterised in detail for all the adsorbent-adsorbate complexes. The results show that these materials are excellent COCl2 adsorbents, with adsorption energies of up to 1.1 eV/molecule and remarkable changes in the electronic properties. The changes in the adsorption stability in a co-adsorption regime indicates that TiG and CrG are efficient adsorbents at low and high relative COCl2 concentrations; while, AlG, MnG and FeG will be efficient only at low relative COCl2 concentrations, where the adsorption stability per COCl2 molecule significantly decreases with respect to the single adsorption. Otherwise, the COCl2 adsorption and electronic response in aerobic environments was found to be suitable only for CrG and MnG, where the electronic response is based on the recognition of the [COCl2]δ+\textendashdopant\textendash[O2]δ− intermediate. This work allows to propose new graphene-based materials for the adsorption, filtration, and/or collection of toxic COCl2.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A density functional theory study was performed to analyse the interaction of COCl2 onto A-doped graphene nanosheets (AG, where A: Al, Si, Ti, Cr, Mn, Fe). Adsorption configurations, adsorption energies, electronic properties, and the interaction in a co-adsorption regime were characterised in detail for all the adsorbent-adsorbate complexes. The results show that these materials are excellent COCl2 adsorbents, with adsorption energies of up to 1.1 eV/molecule and remarkable changes in the electronic properties. The changes in the adsorption stability in a co-adsorption regime indicates that TiG and CrG are efficient adsorbents at low and high relative COCl2 concentrations; while, AlG, MnG and FeG will be efficient only at low relative COCl2 concentrations, where the adsorption stability per COCl2 molecule significantly decreases with respect to the single adsorption. Otherwise, the COCl2 adsorption and electronic response in aerobic environments was found to be suitable only for CrG and MnG, where the electronic response is based on the recognition of the [COCl2]δ+–dopant–[O2]δ− intermediate. This work allows to propose new graphene-based materials for the adsorption, filtration, and/or collection of toxic COCl2. |
Travisany, Dante; Ayala-Raso, Anibal; Genova, Alex Di; Monsalve, Liliam; Bernales, Maricarmen; Martínez, Juan Pablo; González-Agüero, Mauricio; Defilippi, Bruno; Cherian, Sam; Maass, Alejandro; Fuentes, Lida Scientia Horticulturae, 254 , pp. 26 - 34, 2019, ISSN: 0304-4238. @article{TRAVISANY201926, title = {RNA-Seq analysis and transcriptome assembly of raspberry fruit (Rubus idaeus ¨Heritage¨) revealed several candidate genes involved in fruit development and ripening}, author = {Dante Travisany and Anibal Ayala-Raso and Alex Di Genova and Liliam Monsalve and Maricarmen Bernales and Juan Pablo Mart\'{i}nez and Mauricio Gonz\'{a}lez-Ag\"{u}ero and Bruno Defilippi and Sam Cherian and Alejandro Maass and Lida Fuentes}, url = {http://www.sciencedirect.com/science/article/pii/S0304423819302663}, doi = {https://doi.org/10.1016/j.scienta.2019.04.018}, issn = {0304-4238}, year = {2019}, date = {2019-01-01}, journal = {Scientia Horticulturae}, volume = {254}, pages = {26 - 34}, abstract = {Using Illumina HiSeq ™ 2000 sequencing platform (100 bp double-end reads), we performed transcriptome analysis of flower (F), green (G) and pink (P) fruit stages of red raspberry. Transcriptome was obtained by the de-novo assembly of 298 Million high-quality reads through Trinity assembler, out of the 41,650 high quality transcripts, 18,171 coding sequences were successfully characterized using databases such as UniProtKB, NCBI Non-Redundant, KEGG, Gene Ontology, and InterPro-Scan. A total of 2409 transcripts were further identified as differentially expressed genes (DEGs) between the three libraries generated, and 253 DEGs were found between different fruit stages. Singular enrichment analysis of gene ontology (GO) detected an important group of DEGs over-expressed during fruit development; and associated with ethylene, auxin conjugation, abscisic acid response, brassinosteroids biosynthesis and signaling, and cell-wall disassembly processes. Our transcriptome data provides valuable insights on genes involved in the ripening process of Rubus fruit, as a representative of non-model fruit species, and may help in developing these cultivars with improved fruit quality characteristics in the years to come.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Using Illumina HiSeq ™ 2000 sequencing platform (100 bp double-end reads), we performed transcriptome analysis of flower (F), green (G) and pink (P) fruit stages of red raspberry. Transcriptome was obtained by the de-novo assembly of 298 Million high-quality reads through Trinity assembler, out of the 41,650 high quality transcripts, 18,171 coding sequences were successfully characterized using databases such as UniProtKB, NCBI Non-Redundant, KEGG, Gene Ontology, and InterPro-Scan. A total of 2409 transcripts were further identified as differentially expressed genes (DEGs) between the three libraries generated, and 253 DEGs were found between different fruit stages. Singular enrichment analysis of gene ontology (GO) detected an important group of DEGs over-expressed during fruit development; and associated with ethylene, auxin conjugation, abscisic acid response, brassinosteroids biosynthesis and signaling, and cell-wall disassembly processes. Our transcriptome data provides valuable insights on genes involved in the ripening process of Rubus fruit, as a representative of non-model fruit species, and may help in developing these cultivars with improved fruit quality characteristics in the years to come. |
Montecinos, Rodrigo; Gazitúa, Marcela; Santos, José G New J. Chem., 43 , pp. 6372-6379, 2019. @article{C9NJ00385A, title = {The effect of the electrophilic group on the hierarchy of nucleofuges in the aminolysis reactions of thiol- and dithiocarbonates with secondary alicyclic amines: A kinetic and theoretical study}, author = {Rodrigo Montecinos and Marcela Gazit\'{u}a and Jos\'{e} G Santos}, url = {http://dx.doi.org/10.1039/C9NJ00385A}, doi = {10.1039/C9NJ00385A}, year = {2019}, date = {2019-01-01}, journal = {New J. Chem.}, volume = {43}, pages = {6372-6379}, publisher = {The Royal Society of Chemistry}, abstract = {The aminolysis reactions of O-(4-nitrophenyl) S-aryl dithiocarbonates with different secondary alicyclic amines (SAA) lead to the formation of different 4-nitrophenyl : S-aryl ratios (56 : 44 and 47 : 53 for benzenethiol and 4-chlorobenzenethiol, respectively). For the corresponding thiolcarbonates, 4-nitrophenol was the lone product, evidencing the effect of the electrophile moiety on the nucleofugacity hierarchy. The kinetic results show that in the mechanism there are two tetrahedral intermediates: one zwitterionic (T±) and one anionic (T−). As model reactions, the reactions of O-(4-nitrophenyl) S-phenyl thiol- and dithiocarbonates with morpholine were theoretically examined using DFT methods. Theoretical calculations were performed using a continuous solvation model in the absence and presence of one and two explicit water molecules. The microsolvation of T− by one explicit water molecule was predicted as having O-(4-nitrophenyl) : S-phenyl distributions of 52 : 48 and 98 : 2 for dithiocarbonates and thiolcarbonates, respectively. These results have allowed us to establish that processes such as microsolvation, electronic distribution and the structure of the reactive centers participate in the departure of the leaving groups in the thiolcarbonate and dithiocarbonate aminolysis, although the preferential solvation of these centers seems to have a predominant role in the nucleofuge hierarchy.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The aminolysis reactions of O-(4-nitrophenyl) S-aryl dithiocarbonates with different secondary alicyclic amines (SAA) lead to the formation of different 4-nitrophenyl : S-aryl ratios (56 : 44 and 47 : 53 for benzenethiol and 4-chlorobenzenethiol, respectively). For the corresponding thiolcarbonates, 4-nitrophenol was the lone product, evidencing the effect of the electrophile moiety on the nucleofugacity hierarchy. The kinetic results show that in the mechanism there are two tetrahedral intermediates: one zwitterionic (T±) and one anionic (T−). As model reactions, the reactions of O-(4-nitrophenyl) S-phenyl thiol- and dithiocarbonates with morpholine were theoretically examined using DFT methods. Theoretical calculations were performed using a continuous solvation model in the absence and presence of one and two explicit water molecules. The microsolvation of T− by one explicit water molecule was predicted as having O-(4-nitrophenyl) : S-phenyl distributions of 52 : 48 and 98 : 2 for dithiocarbonates and thiolcarbonates, respectively. These results have allowed us to establish that processes such as microsolvation, electronic distribution and the structure of the reactive centers participate in the departure of the leaving groups in the thiolcarbonate and dithiocarbonate aminolysis, although the preferential solvation of these centers seems to have a predominant role in the nucleofuge hierarchy. |
Montenegro-Pohlhammer, Nicolás; Urzua-Leiva, Rodrigo; Páez-Hernández, Dayán; Cardenas-Jiron, Gloria Spin-filter transport and magnetic properties in binuclear Cu(II) expanded porphyrin based molecular junction Journal Article Dalton Trans., pp. -, 2019. @article{C9DT01312A, title = {Spin-filter transport and magnetic properties in binuclear Cu(II) expanded porphyrin based molecular junction}, author = {Nicol\'{a}s Montenegro-Pohlhammer and Rodrigo Urzua-Leiva and Day\'{a}n P\'{a}ez-Hern\'{a}ndez and Gloria Cardenas-Jiron}, url = {http://dx.doi.org/10.1039/C9DT01312A}, doi = {10.1039/C9DT01312A}, year = {2019}, date = {2019-01-01}, journal = {Dalton Trans.}, pages = {-}, publisher = {The Royal Society of Chemistry}, abstract = {Although the magnetic and transport properties of molecular junction systems composed of metalled porphyrins or phthalocyanines have been broadly studied in recent years, to date no studies have been devoted to evaluate the aforementioned properties in junction systems featuring metalled expanded porphyrins as active elements. The present work reports a detailed theoretical study of the magnetic and electronic transport properties of the recently synthesized dinuclear Cu(II)-Naphthoisoamethyrin complex (PyCu2). This is the first work on performing these kinds of studies using a magnetically-coupled metallic expanded porphyrin as molecular kernel. DFT and wave function-based methods have been used to determine the nature of the magnetic interaction between the metallic centres, characterized by the exchange coupling constant J, showing that although this was attributed to be weakly antiferromagnetic, after an exhaustive analysis it turns out that the coupling has a ferromagnetic nature with a value of J = 14.2 cm-1. Once the magnetic ground state of PyCu2 was rigorously established, the spin resolved transport properties of the device composed on the expanded porphyrin attached to two gold nano-wires were studied by means of the combination of DFT and nonequilibrium Green´s function formalism, in order to explore PyCu2 prospects as a possible spintronic device.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Although the magnetic and transport properties of molecular junction systems composed of metalled porphyrins or phthalocyanines have been broadly studied in recent years, to date no studies have been devoted to evaluate the aforementioned properties in junction systems featuring metalled expanded porphyrins as active elements. The present work reports a detailed theoretical study of the magnetic and electronic transport properties of the recently synthesized dinuclear Cu(II)-Naphthoisoamethyrin complex (PyCu2). This is the first work on performing these kinds of studies using a magnetically-coupled metallic expanded porphyrin as molecular kernel. DFT and wave function-based methods have been used to determine the nature of the magnetic interaction between the metallic centres, characterized by the exchange coupling constant J, showing that although this was attributed to be weakly antiferromagnetic, after an exhaustive analysis it turns out that the coupling has a ferromagnetic nature with a value of J = 14.2 cm-1. Once the magnetic ground state of PyCu2 was rigorously established, the spin resolved transport properties of the device composed on the expanded porphyrin attached to two gold nano-wires were studied by means of the combination of DFT and nonequilibrium Green´s function formalism, in order to explore PyCu2 prospects as a possible spintronic device. |
Sandoval, Jorge; Mignot, Emmanuel; Mao, Luca; Pastén, Pablo; Bolster, Diogo; Escauriaza, Cristián Field and Numerical Investigation of Transport Mechanisms in a Surface Storage Zone Journal Article Journal of Geophysical Research: Earth Surface, 124 (4), pp. 938–959, 2019. @article{Sandoval2019, title = {Field and Numerical Investigation of Transport Mechanisms in a Surface Storage Zone}, author = {Jorge Sandoval and Emmanuel Mignot and Luca Mao and Pablo Past\'{e}n and Diogo Bolster and Cristi\'{a}n Escauriaza}, url = {https://doi.org/10.1029/2018jf004716}, doi = {10.1029/2018jf004716}, year = {2019}, date = {2019-01-01}, journal = {Journal of Geophysical Research: Earth Surface}, volume = {124}, number = {4}, pages = {938--959}, publisher = {American Geophysical Union (AGU)}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Hermann-Avigliano, C; Salinas, I A; Rivas, D A; Real, B; Mančić, A; Mejía-Cortés, C; Maluckov, A; Vicencio, R A Spatial rogue waves in photorefractive SBN crystals Journal Article Opt. Lett., 44 (11), pp. 2807–2810, 2019. @article{hermann-avigliano_spatial_2019, title = {Spatial rogue waves in photorefractive SBN crystals}, author = {C Hermann-Avigliano and I A Salinas and D A Rivas and B Real and A Man\v{c}i\'{c} and C Mej\'{i}a-Cort\'{e}s and A Maluckov and R A Vicencio}, url = {http://ol.osa.org/abstract.cfm?URI=ol-44-11-2807}, doi = {10.1364/OL.44.002807}, year = {2019}, date = {2019-01-01}, journal = {Opt. Lett.}, volume = {44}, number = {11}, pages = {2807--2810}, abstract = {We report on the excitation of large-amplitude waves, with a probability of around 1% of total peaks, on a photorefractive SBN crystal by using a simple experimental setup at room temperature. We excite the system using a narrow Gaussian beam and observe different dynamical regimes tailored by the value and time rate of an applied voltage. We identify two main dynamical regimes: a caustic one for energy spreading and a speckling one for peak emergence. Our observations are well described by a two-dimensional Schrödinger model with saturable local nonlinearity.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report on the excitation of large-amplitude waves, with a probability of around 1% of total peaks, on a photorefractive SBN crystal by using a simple experimental setup at room temperature. We excite the system using a narrow Gaussian beam and observe different dynamical regimes tailored by the value and time rate of an applied voltage. We identify two main dynamical regimes: a caustic one for energy spreading and a speckling one for peak emergence. Our observations are well described by a two-dimensional Schrödinger model with saturable local nonlinearity. |
Wu, Xiaobo; Zhang, Wenjuan; Morales-Verdejo, Cesar; Sheng, Yingying; Camarada, María Belén; Chen, Li; Huang, Zhong; Wen, Yangping Nanohybrid sensor for simple, cheap, and sensitive electrochemical recognition and detection of methylglyoxal as chemical markers Journal Article Journal of Electroanalytical Chemistry, 839 , pp. 177 - 186, 2019, ISSN: 1572-6657. @article{WU2019177, title = {Nanohybrid sensor for simple, cheap, and sensitive electrochemical recognition and detection of methylglyoxal as chemical markers}, author = {Xiaobo Wu and Wenjuan Zhang and Cesar Morales-Verdejo and Yingying Sheng and Mar\'{i}a Bel\'{e}n Camarada and Li Chen and Zhong Huang and Yangping Wen}, url = {http://www.sciencedirect.com/science/article/pii/S1572665719301833}, doi = {https://doi.org/10.1016/j.jelechem.2019.03.022}, issn = {1572-6657}, year = {2019}, date = {2019-01-01}, journal = {Journal of Electroanalytical Chemistry}, volume = {839}, pages = {177 - 186}, abstract = {We successfully designed a nanohybrid sensor based on carboxyl-functionalized multi-walled carbon nanotubes (MWCNTs-COOH) co-functionalized with both carboxymethyl cellulose (CMC) and chitosan nanosphere (CSN) for a simple, low-cost, highly-sensitive voltammetric recognition and determination of Methylglyoxal (MG) as chemical marker of New Zealand Manuka honey. Morphology and structure revealed that CSN-CMC was adhered onto MWCNTs-COOH surface. Interactions between modifying layers and both reduction potential and response mechanism of MG were confirmed by theoretical calculations. The nanohybrid sensor displayed large electrochemical effective area, excellent electrocatalytic activity, a wide linear range of 5×10−8\textendash8×10−4mol/L, a low detection limit of 9.6×10−9mol/L, and good stability as well as selectivity under the optimal conditions. The applicability of the fabricated sensor was assessed using three Chinese honeys and one New Zealand Manuka honey. This work will put forward a new strategy for electrochemical recognition and detection of MG as chemical markers of many agricultural production, processing, products and food and a new alternative tool for assessing economically motivated fraud and counterfeit issues in Chinese honey markets using electrochemical nanohybrid sensor.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We successfully designed a nanohybrid sensor based on carboxyl-functionalized multi-walled carbon nanotubes (MWCNTs-COOH) co-functionalized with both carboxymethyl cellulose (CMC) and chitosan nanosphere (CSN) for a simple, low-cost, highly-sensitive voltammetric recognition and determination of Methylglyoxal (MG) as chemical marker of New Zealand Manuka honey. Morphology and structure revealed that CSN-CMC was adhered onto MWCNTs-COOH surface. Interactions between modifying layers and both reduction potential and response mechanism of MG were confirmed by theoretical calculations. The nanohybrid sensor displayed large electrochemical effective area, excellent electrocatalytic activity, a wide linear range of 5×10−8–8×10−4mol/L, a low detection limit of 9.6×10−9mol/L, and good stability as well as selectivity under the optimal conditions. The applicability of the fabricated sensor was assessed using three Chinese honeys and one New Zealand Manuka honey. This work will put forward a new strategy for electrochemical recognition and detection of MG as chemical markers of many agricultural production, processing, products and food and a new alternative tool for assessing economically motivated fraud and counterfeit issues in Chinese honey markets using electrochemical nanohybrid sensor. |
Miño-Galaz, Germán; Gonzalez, Jose Mauricio; Staforelli, Juan Pablo; Gutierrez, Gonzalo Asymmetrical vibrational energy propagation through double or single bonds of small organic molecules. An ab-initio molecular dynamics study Journal Article Chemical Physics Letters, 2019. @article{MioGalaz2019, title = {Asymmetrical vibrational energy propagation through double or single bonds of small organic molecules. An ab-initio molecular dynamics study}, author = {Germ\'{a}n Mi\~{n}o-Galaz and Jose Mauricio Gonzalez and Juan Pablo Staforelli and Gonzalo Gutierrez}, url = {https://doi.org/10.1016/j.cplett.2019.05.056}, doi = {10.1016/j.cplett.2019.05.056}, year = {2019}, date = {2019-01-01}, journal = {Chemical Physics Letters}, publisher = {Elsevier BV}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
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