Publicaciones

@article{Yáñez2020,
title = {High-Throughput Single Nucleotide Polymorphism (SNP) Discovery and Validation Through Whole-Genome Resequencing in Nile Tilapia (Oreochromis niloticus)},
author = {Jose M Yanez and Grazyella Yoshida and Agustin Barria and Ricardo Palma-Vejares and Dante Travisany and Diego Diaz and Giovanna Caceres and Maria I Cadiz and Maria E Lopez and Jean P Lhorente and Ana Jedlicki and Jose Soto and Diego Salas and Alejandro Maass},
url = {https://doi.org/10.1007/s10126-019-09935-5},
doi = {10.1007/s10126-019-09935-5},
issn = {1436-2236},
year = {2020},
date = {2020-01-14},
journal = {Marine Biotechnology},
abstract = {Nile tilapia (Oreochromis niloticus) is the second most important farmed fish in the world and a sustainable source of protein for human consumption. Several genetic improvement programs have been established for this species in the world. Currently, the estimation of genetic merit of breeders is typically based on genealogical and phenotypic information. Genome-wide information can be exploited to efficiently incorporate traits that are difficult to measure into the breeding goal. Thus, single nucleotide polymorphisms (SNPs) are required to investigate phenotype--genotype associations and determine the genomic basis of economically important traits. We performed de novo SNP discovery in three different populations of farmed Nile tilapia. A total of 29.9 million non-redundant SNPs were identified through Illumina (HiSeq 2500) whole-genome resequencing of 326 individual samples. After applying several filtering steps, including removing SNP based on genotype and site quality, presence of Mendelian errors, and non-unique position in the genome, a total of 50,000 high-quality SNPs were selected for the development of a custom Illumina BeadChip SNP panel. These SNPs were highly informative in the three populations analyzed showing between 43,869 (94%) and 46,139 (99%) SNPs in Hardy-Weinberg Equilibrium; 37,843 (76%) and 45,171(90%) SNPs with a minor allele frequency (MAF) higher than 0.05; and 43,450 (87%) and 46,570 (93%) SNPs with a MAF higher than 0.01. The 50K SNP panel developed in the current work will be useful for the dissection of economically relevant traits, enhancing breeding programs through genomic selection, as well as supporting genetic studies in farmed populations of Nile tilapia using dense genome-wide information.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{GallardoFuentes2020,
title = {Theoretical insights into the activation of N2O by a model Frustrated Lewis Pair. An Ab-Initio Metadynamics study},
author = {Sebastian Gallardo-Fuentes and Rodrigo Ormazabal-Toledo},
url = {https://doi.org/10.1016/j.cplett.2019.137002},
doi = {10.1016/j.cplett.2019.137002},
year = {2020},
date = {2020-01-01},
journal = {Chemical Physics Letters},
pages = {137002},
publisher = {Elsevier BV},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{GonzlezRubio2020,
title = {Formation of Hollow Gold Nanocrystals by Nanosecond Laser Irradiation},
author = {Guillermo Gonzalez-Rubio and Thais Milagres de Oliveira and Wiebke Albrecht and Pablo Diaz-Nunez and Juan Carlos Castro-Palacio and Alejandro Prada and Rafael I Gonzalez and Leonardo Scarabelli and Luis Banares and Antonio Rivera and Luis M Liz-Marzan and Ovidio Pena-Rodriguez and Sara Bals and Andres Guerrero-Martinez},
url = {https://doi.org/10.1021/acs.jpclett.9b03574},
doi = {10.1021/acs.jpclett.9b03574},
year = {2020},
date = {2020-01-01},
journal = {The Journal of Physical Chemistry Letters},
publisher = {American Chemical Society (ACS)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{CceresSoto2020,
title = {Comparison of QuikSCAT, WRF and buoy ocean surface wind data off Valparaiso Bay, Chile},
author = {M Cáceres-Soto and H H Sepúlveda and K Muñoz-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}
}

@article{RosGonzlez2020,
title = {Inducing a level inside of CdTe bandgap doping with Sn using a co-sublimation technique by CSS},
author = {J A R í and R Mis-Fernández and E Camacho-Espinosa and I Riech and E Menéndez-Proupin and M A Flores and W Orellana and J L Peña},
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}
}

@article{THIERS2020106245,
title = {Heat transfer enhancement by localised time varying thermal perturbations at hot and cold walls in a rectangular differentially heated cavity},
author = {N Thiers and R Gers and O Skurtys},
url = {http://www.sciencedirect.com/science/article/pii/S1290072919313997},
doi = {https://doi.org/10.1016/j.ijthermalsci.2019.106245},
issn = {1290-0729},
year = {2020},
date = {2020-01-01},
journal = {International Journal of Thermal Sciences},
volume = {151},
pages = {106245},
abstract = {The objective of this work it is to determine the optimal properties of a thermal disturbance to enhance the heat transfer in a rectangular differentially heated cavity of aspect ratio 4. So, we study numerically the effect on the heat transfer of one or two small thermal actuators (5% of active plate surface) applied at the active walls of this kind of cavity. Thermal disturbances are sine or square waves. Influences of wave characteristics (amplitude, frequency, phase shift) and the vertical location of the disturbance area are investigated for various Rayleigh numbers below its first critical value (RaH=1.02×108). Only a fluid with Prandtl number equal to 0.71 (air) is considered. Flows are calculated solving the 2D unsteady Boussinesq–Navier–Stokes equations using the Spectral Element Method programmed in the Nek5000 opencode. A detailed description of the coupling between one or two thermal disturbances and cavity flow is presented. The main contribution of this work is that the best position to enhance the heat transfer is 70% of the hot plate height or 30% of the cold plate height, and not 0.1 for the hot plate (0.9 for the cold one) which is generally admitted. At this position this increase reaches 5.5% by disturbing at both active walls with local synchronised square waves of amplitude ε=1, of frequency f=0.403 and at a state slightly below the first critical Rayleigh number.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Urbina2020,
title = {Equilibrium and nonequilibrium in the three-dimensional Q2R cellular automata},
author = {Felipe Urbina},
url = {https://doi.org/10.1103/physreve.101.012111},
doi = {10.1103/physreve.101.012111},
year = {2020},
date = {2020-01-01},
journal = {Physical Review E},
volume = {101},
number = {1},
publisher = {American Physical Society (APS)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Urbina2020b,
title = {Equilibrium and nonequilibrium in the three-dimensional Q2R cellular automata},
author = {Felipe Urbina},
url = {https://doi.org/10.1103/physreve.101.012111},
doi = {10.1103/physreve.101.012111},
year = {2020},
date = {2020-01-01},
journal = {Physical Review E},
volume = {101},
number = {1},
publisher = {American Physical Society (APS)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000508208600001,
title = {Modeling the effects of sediment concentration on the propagation of
flash floods in an Andean watershed},
author = {Maria Teresa Contreras and Cristian Escauriaza},
doi = {10.5194/nhess-20-221-2020},
issn = {1561-8633},
year = {2020},
date = {2020-01-01},
journal = {NATURAL HAZARDS AND EARTH SYSTEM SCIENCES},
volume = {20},
number = {1},
pages = {221-241},
abstract = {Rain-induced flash floods are common events in regions near mountain
ranges. In peri-urban areas near the Andes the combined effects of the
changing climate and El Nifio-Southern Oscillation (ENSO) have resulted
in an alarming proximity of populated areas to flood-prone streams,
increasing the risk for cities and infrastructure. Simulations of rapid
floods in these watersheds are particularly challenging, due to the
complex morphology, the insufficient hydrometeorological data, and the
uncertainty posed by the variability of sediment concentration. High
concentrations produced by hillslope erosion and rilling by the overland
flow in areas with steep slopes and low vegetational covering can
significantly change the dynamics of the flow as the flood propagates in
the channel. In this investigation, we develop a two-dimensional
finite-volume numerical model of the nonlinear shallow water equations
coupled with the mass conservation of sediment to study the effects of
different densities, which include a modified version of the quadratic
stress model to quantify the changes in the flow rheology. We carry out
simulations to evaluate the effects of the sediment concentration on the
floods in the Quebrada de Ramon watershed, a peri-urban Andean basin in
central Chile. We simulate a confluence and a total length of the
channel of 10.4 km, with the same water hydrographs and different
combinations of sediment concentrations in the tributaries. Our results
show that the sediment concentration has strong impacts on flow
velocities and water depths. Compared to clearwater flow, the wave-front
velocity slows down more than 70 % for floods with a volumetric
concentration of 60 % and the total flooded area is 36 % larger when
the sediment concentration is equal to 20 %. The maximum flow momentum
at cross sections in the urban area increases 14.5 % on average when
the mean concentration along the main channel changes from 30 % to 44
%. Simulations also show that other variables such as the arrival time
of the peak flow and the shape of the hydrograph at different locations
along the channel are not significantly affected by the sediment
concentration and depend mostly on the steep channel morphology. Through
this work we provide a framework for future studies aimed at improving
hazard assessment, urban planning, and early warning systems in urban
areas near mountain streams with limited data and affected by rapid
flood events.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Viera2020,
title = {Oxygen Reduction Reaction at Penta-Coordinated Co Phthalocyanines},
author = {Marco Viera and Jorge Riquelme and Carolina Aliaga and Jose F Marco and Walter Orellana and Jose H Zagal and Federico Tasca},
url = {https://doi.org/10.3389/fchem.2020.00022},
doi = {10.3389/fchem.2020.00022},
year = {2020},
date = {2020-01-01},
journal = {Frontiers in Chemistry},
volume = {8},
publisher = {Frontiers Media SA},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Viera2020b,
title = {Magnon valley Hall effect in CrI3-based vdW heterostructures},
author = {Vogel Allende Mella Jose Cardenas Troncoso Roberto Munoz R I E E S D C E F Hidalgo-Sacoto R Gonzalez},
url = {https://arxiv.org/pdf/2001.11934.pdf},
doi = {arXiv:2001.11934v1},
year = {2020},
date = {2020-01-01},
journal = {arxiv.org},
volume = {1},
publisher = {arxiv.org},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000492034800004,
title = {A column generation approach to multiscale capacity planning for
power-intensive process networks},
author = {Angela Flores-Quiroz and Jose M Pinto and Qi Zhang},
doi = {10.1007/s11081-019-09435-4},
issn = {1389-4420},
year = {2019},
date = {2019-12-01},
journal = {OPTIMIZATION AND ENGINEERING},
volume = {20},
number = {4, SI},
pages = {1001-1027},
abstract = {Due to the high volatility in electricity prices, power-intensive
industrial plants often have to frequently shift load in order to remain
cost-competitive. Capacity planning is required for assessing the value
of additional operational flexibility and planning for expected changes
in product demand. Here, the main challenge lies in the simultaneous
consideration of long-term capacity planning and short-term operational
decisions. In this work, we extend the multiscale model proposed by
Mitra et al. (Comput Chem Eng 65:89-101, 2014a) to a formulation that
applies a general process network representation and incorporates
inventory handling across seasons. We propose a column generation
approach to solve large instances of the resulting mixed-integer linear
program (MILP). The algorithm decomposes the original problem into
multiple MILP subproblems, while the restricted master problem is an
integer program. Computational experiments demonstrate the effectiveness
of the column generation algorithm, which clearly outperforms the
full-space model, especially with increasing number of years in the
planning horizon. Also, the results show that the master problem tends
to yield integer solutions within the required optimality gap due to its
strong linear programming relaxation, such that no further branching is
required. Moreover, the proposed approach is applied to perform capacity
planning for a real-world industrial air separation plant.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000496150500007,
title = {In search of the most active MN4 catalyst for the oxygen reduction
reaction. The case of perfluorinated Fe phthalocyanine},
author = {Gabriel Abarca and Marco Viera and Carolina Aliaga and Jose F Marco and Walter Orellana and Jose H Zagal and Federico Tasca},
doi = {10.1039/c9ta09125d},
issn = {2050-7488},
year = {2019},
date = {2019-11-01},
journal = {JOURNAL OF MATERIALS CHEMISTRY A},
volume = {7},
number = {43},
pages = {24776-24783},
abstract = {Iron macrocyclic complexes (MN4) are promising catalysts for replacing
platinum (the industrial standard) in electrocatalysis. In particular,
FeN4 complexes have shown lower overpotential than Pt for the oxygen
reduction reaction (ORR) in alkaline media. To predict the
electrochemical activity of metal electrodes and molecular catalysts
towards the ORR, reactivity descriptors with typical volcano correlation
have been demonstrated. The most important are M-O-2 binding energy and
M(n)+/M(n-1)+ redox potentials for the complexes. We studied a new Fe
complex, which possesses powerful electron-withdrawing fluorine residues
at the periphery of the phthalocyanine ring. Fe
hexadecafluorophthalocyanine (16(F)FePc) was characterized by electron
paramagnetic resonance (EPR), and X-ray photoelectron spectroscopy (XPS)
in the presence and in absence of O-2. Experimental and calculated
O-2-Fe binding energies, as well as electrochemical characterization
confirms the excellent activity of this complex for the ORR placing this
complex at the top of the MN4 volcano correlation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000499868900001,
title = {The Role of Gas Fragmentation During the Formation of Supermassive Black
Holes},
author = {Matias Suazo and Joaquin Prieto and Andres Escala and Dominik Schleicher},
doi = {10.3847/1538-4357/ab45eb},
issn = {0004-637X},
year = {2019},
date = {2019-11-01},
journal = {ASTROPHYSICAL JOURNAL},
volume = {885},
number = {2},
abstract = {We perform cosmological hydrodynamic simulations to study the effect of
gas fragmentation on the formation of supermassive black hole seeds in
the context of Direct Collapse. Our setup considers different UV
background intensities, host halo spins, and halo merger histories. We observe that our low-spin halos are consistent with the Direct Collapse model when they are irradiated by a UV background of J(21) = 10,000. In
these cases, a single massive object ?10(5) M is formed in the center of the halo. On the other hand, in our simulations irradiated by a UV background of J(21) = 10, we see fragmentation and the formation of
various less massive seeds. These fragments have masses of 10(3)?10(4)
M. These values are still 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. Moreover,
in one of our simulations, we observe gas fragmentation even in the
presence of a strong UV intensity. This structure arises in a dark
matter halo that forms after various merger episodes, becoming the
structure with the highest spin value. The final black hole seed mass is
?10(5) M for this run. From these results, we conclude that
fragmentation produces less massive objects; however, they are still
prone to merge. In simulations that form many fragments, they all
approach the most massive one as the simulations evolve. We see no
uniqueness in the strength of the UV intensity value required to form a
DCBH since it depends on other factors like the system dynamics in our
cases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000501529700019,
title = {Evaluation of the Anti-Diabetic Activity of Some Common Herbs and
Spices: Providing New Insights with Inverse Virtual Screening},
author = {Andreia S P Pereira and Antonio J Banegas-Luna and Jorge Pena-Garcia and Horacio Perez-Sanchez and Zeno Apostolides},
doi = {10.3390/molecules24224030},
year = {2019},
date = {2019-11-01},
journal = {MOLECULES},
volume = {24},
number = {22},
abstract = {Culinary herbs and spices are widely used as a traditional medicine in
the treatment of diabetes and its complications, and there are several
scientific studies in the literature supporting the use of these
medicinal plants. However, there is often a lack of knowledge on the
bioactive compounds of these herbs and spices and their mechanisms of
action. The aim of this study was to use inverse virtual screening to
provide insights into the bioactive compounds of common herbs and
spices, and their potential molecular mechanisms of action in the
treatment of diabetes. In this study, a library of over 2300 compounds
derived from 30 common herbs and spices were screened in silico with the
DIA-DB web server against 18 known diabetes drug targets. Over 900
compounds from the herbs and spices library were observed to have
potential anti-diabetic activity and liquorice, hops, fennel, rosemary,
and fenugreek were observed to be particularly enriched with potential
anti-diabetic compounds. A large percentage of the compounds were
observed to be potential polypharmacological agents regulating three or
more anti-diabetic drug targets and included compounds such as achillin
B from yarrow, asparasaponin I from fenugreek, bisdemethoxycurcumin from
turmeric, carlinoside from lemongrass, cinnamtannin B1 from cinnamon,
crocin from saffron and glabridin from liquorice. The major targets
identified for the herbs and spices compounds were dipeptidyl
peptidase-4 (DPP4), intestinal maltase-glucoamylase (MGAM), liver
receptor homolog-1 (NR5A2), pancreatic alpha-amylase (AM2A), peroxisome
proliferator-activated receptor alpha (PPARA), protein tyrosine
phosphatase non-receptor type 9 (PTPN9), and retinol binding protein-4
(RBP4) with over 250 compounds observed to be potential inhibitors of
these particular protein targets. Only bay leaves, liquorice and thyme
were found to contain compounds that could potentially regulate all 18
protein targets followed by black pepper, cumin, dill, hops and marjoram
with 17 protein targets. In most cases more than one compound within a
given plant could potentially regulate a particular protein target. It
was observed that through this multi-compound-multi target regulation of
these specific protein targets that the major anti-diabetic effects of
reduced hyperglycemia and hyperlipidemia of the herbs and spices could
be explained. The results of this study, taken together with the known
scientific literature, indicated that the anti-diabetic potential of
common culinary herbs and spices was the result of the collective action
of more than one bioactive compound regulating and restoring several
dysregulated and interconnected diabetic biological processes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{González2019b,
title = {A hybrid deterministic and stochastic approach for tsunami hazard assessment in Iquique, Chile},
author = {Juan González and Gabriel González and Rafael Aránguiz and Diego Melgar and Natalia Zamora and Mahesh N Shrivastava and Ranjit Das and Patricio A Catalán 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--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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@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}
}

@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}
}

@article{ISI:000492803300013,
title = {Water Flow in Silica Nanopores Coated by Carbon Nanotubes from a Wetting
Translucency Perspective},
author = {Enrique Wagemann and Jens H Walther and Eduardo R Cruz-Chu and Harvey A Zambrano},
doi = {10.1021/acs.jpcc.9b05294},
issn = {1932-7447},
year = {2019},
date = {2019-10-01},
journal = {JOURNAL OF PHYSICAL CHEMISTRY C},
volume = {123},
number = {42},
pages = {25635-25642},
abstract = {Nearly frictionless water transport makes carbon nanotubes promising
materials for use as conduits in nanofluidic applications. Here, we
conduct molecular dynamics simulations of water flow within amorphous
silica nanopores coated by a (39,39) single-walled carbon nanotube
(SWCNT). Our atomistic models describe the interaction between water and
pore walls based on two possible scenarios, translucency and opacity to
wetting of a SWCNT. Simulation results indicate that the SWCNT coating
enhances water flow through silica pores ca. 10 times compared to
predictions from the classical Hagen-Poiseuille relation. By varying the
strength of the water-pore interaction, we study the relationship
between surface wettability and hydrodynamic slippage. We observe an
increase in the slip length for higher values of water contact angle.
Moreover, cases with SWCNT opacity and translucency to wetting display a
substantial difference in the computed slippage, showing that the water
contact angle is not the only factor that determines the slip boundary
condition under nanoconfinement. We attribute this disparity to the
corrugation of the potential energy landscape at the inner pore wall.
The present study provides a theoretical framework for the use of carbon
nanotube-based coatings in designing more efficient nanofluidic
conduits.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@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}
}

@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 René Ruby-Figueroa and Humberto Estay and Diego Cortés-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}
}

@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 René 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}
}

@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 Muñoz 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}
}

@article{Bossy2019,
title = {Synchronization of stochastic mean field networks of Hodgkin--Huxley neurons with noisy channels},
author = {Mireille Bossy and Joaquín Fontbona and Héctor 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}
}

@article{Schmidt_2019,
title = {Contribution of digluons to charmonia production},
author = {Iván 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}
}

@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 Elías Figueroa and Patricio Ulloa-Rodríguez and Rommy Díaz and Iván Valdebenito and Jorge G Farías},
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}
}

@article{Jurez2019,
title = {Stability, electronic and optical properties of the boron nitride cage (B47N53) from quantum mechanical calculations},
author = {Rodríguez Ju A á and Borges-Mart M í and Cárdenas-Jir G ó 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}
}

@article{lusarczyk2019,
title = {Selective in vitro and in silico cholinesterase inhibitory activity of isoflavones and stilbenes from Belamcandae chinensis rhizoma},
author = {Sylwester Ś and Sezer Senol F Deniz and Dorota Wo ź and Ł and Horacio Pérez-S á and José Cer P ó 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}
}

@article{Travisany2019,
title = {Generation and robustness of Boolean networks to model Clostridium difficile infection},
author = {Dante Travisany and Eric Goles and Mauricio Latorre and María-Paz Cort é 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}
}

@article{Maza2019,
title = {Soil Bacterial Communities From the Chilean Andean Highlands: Taxonomic Composition and Culturability},
author = {Felipe Maza and Jonathan Maldonado and Javiera V á and Dinka Mandakovic and Alexis Gaete and Ver ó and Mauricio Gonz á},
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}
}

@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 Héctor Sep H ú},
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}
}

@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 á 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}
}

@article{Duli2019,
title = {Single-Molecule Transport of Fullerene-Based Curcuminoids},
author = {Diana Duli ć and Alfredo Rates and Edison Castro and Jacqueline Labra-Munoz and Daniel Aravena and Alvaro Etcheverry-Berrios and Daniel Riba-Lopez and Eliseo Ruiz and Nuria Aliaga-Alcalde and Monica Soler and Luis Echegoyen and Herre S J van der Zant},
url = {https://doi.org/10.1021/acs.jpcc.9b10166},
doi = {10.1021/acs.jpcc.9b10166},
year = {2019},
date = {2019-01-01},
journal = {The Journal of Physical Chemistry C},
publisher = {American Chemical Society (ACS)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Duli2019b,
title = {A Deep Learning Model for Chilean Bills Classification},
author = {Daniel San Martin and Daniel Manzano},
url = {https://doi.org/1912.12120v1},
doi = {1912.12120v1},
year = {2019},
date = {2019-01-01},
journal = {Arxiv},
publisher = {Arxiv},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@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 Martínez and Dante Travisany and Bruno Defilippi and Mauricio González-Agüero 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}
}

@techreport{diaz_impact_2019,
title = {Impact of radiation backgrounds on the formation of massive black holes},
author = {VB Díaz 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 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.},
keywords = {},
pubstate = {published},
tppubtype = {techreport}
}

@article{davis_bayesian_2019,
title = {Bayesian statistical modeling of microcanonical melting times at the superheated regime},
author = {Sergio Davis and Claudia Loyola and Joaquín 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}
}

@article{banegas-luna_advances_2019,
title = {Advances in distributed computing with modern drug discovery},
author = {Antonio Jesús Banegas-Luna and Baldomero Imbernón and Antonio Llanes Castro and Alfonso Pérez-Garrido and José Pedro Cerón-Carrasco and Sandra Gesing and Ivan Merelli and Daniele D’Agostino and Horacio Pérez-Sánchez},
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}
}

@article{menendez-proupin_symmetry_2019,
title = {Symmetry and thermodynamics of tellurium vacancies in cadmium telluride},
author = {E Menéndez-Proupin and M Casanova-Páez 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}
}

@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 Martínez-Cifuentes and Matías Monroy-Cárdenas and Juan Pablo Millas-Vargas and Boris E Weiss-López 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}
}

@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}
}

@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}
}

@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 Muñoz 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}
}

@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 Yañez 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}
}

@article{morell_control_2019,
title = {Control of magnetism in bilayer CrI3 by an external electric field},
author = {Suárez E Morell and Andrea León 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 546 270–3; 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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@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 Ríos and Paula Povea and Christopher Cerda-Cavieres and Juan L Arroyo and Cesar Morales-Verdejo and Gabriel Abarca and María 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 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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@techreport{baruteau_dust_2019,
title = {Dust traps in the protoplanetary disc MWC 758: two vortices produced by two giant planets?},
author = {Clément Baruteau and Marcelo Barraza and Sebastián Pérez and Simon Casassus and Ruobing Dong and Wladimir Lyra and Sebastián Marino and Valentin Christiaens and Zhaohuan Zhu and Andrés 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}
}

@article{BRAVO201923,
title = {Genetic diversity and phylogenetic relationship among araucana creole sheep and Spanish sheep breeds},
author = {Silvana Bravo and Giovanni Larama and John Quiñones and Erwin Paz and Evangelina Rodero and Néstor Sepúlveda},
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 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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{lagos-alvarez_kalman_2019,
title = {A Kalman filter method for estimation and prediction of space–time data with an autoregressive structure},
author = {Bernardo Lagos-Álvarez 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–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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@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 Solà and Henry F Schaefer and Alejandro Toro-Labbé},
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–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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@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}
}

@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}
}

@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 Coñuecar and César A Ramírez-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 –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.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{10.1093/mnras/stz220,
title = {Dissecting the active galactic nucleus in Circinus – 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}
}

@article{GAJARDO201971,
title = {Capturing the development and interactions of wakes in tidal turbine arrays using a coupled BEM-DES model},
author = {Daniel Gajardo and Cristián 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}
}

@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–N bond of AB, what is known to produce the poisoning of the catalyst by ammonia generation.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{C9NJ01493D,
title = {σ-Hole promotes the Concertedness in Nucleophilic Aromatic Substitution reactions of nitroarenes},
author = {Sebastián 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}
}

@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 Cortés-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+–dopant–[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}
}

@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 Martínez and Mauricio González-Agüero 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}
}

@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 Gazitúa and José 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}
}