Publicaciones

@article{Guerrero2013,
title = {A performance/cost model for a CUDA drug discovery application on physical and public cloud infrastructures},
author = {Gines D Guerrero and Richard M Wallace and Jose L Vazquez-Poletti and Jose M Cecilia and Jose M Garcia and Daniel Mozos and Horacio Perez-Sanchez},
url = {https://doi.org/10.1002/cpe.3117},
doi = {10.1002/cpe.3117},
year = {2013},
date = {2013-01-01},
journal = {Concurrency and Computation: Practice and Experience},
volume = {26},
number = {10},
pages = {1787--1798},
publisher = {Wiley},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{delValle2013,
title = {BINARY-DISK INTERACTION. II. GAP-OPENING CRITERIA FOR UNEQUAL-MASS BINARIES},
author = {Luciano del Valle and Andres Escala},
url = {https://doi.org/10.1088/0004-637x/780/1/84},
doi = {10.1088/0004-637x/780/1/84},
year = {2013},
date = {2013-01-01},
journal = {The Astrophysical Journal},
volume = {780},
number = {1},
pages = {84},
publisher = {IOP Publishing},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Flores2013d,
title = {CFD simulations of turbulent buoyant atmospheric flows over complex geometry: Solver development in OpenFOAM},
author = {Federico Flores and René9 Garreaud and Ricardo C Mu'f1oz},
url = {https://doi.org/10.1016/j.compfluid.2013.04.029},
doi = {10.1016/j.compfluid.2013.04.029},
year = {2013},
date = {2013-01-01},
journal = {Computers & Fluids},
volume = {82},
pages = {1--13},
publisher = {Elsevier BV},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{CaonMancisidor2012,
title = {Theoretical description of the magnetic properties of $upmu$3-hydroxo bridged trinuclear copper(II) complexes},
author = {Walter Canon-Mancisidor and Evgenia Spodine and Veronica Paredes-Garcia and Diego Venegas-Yazigi},
url = {https://doi.org/10.1007/s00894-012-1696-5},
doi = {10.1007/s00894-012-1696-5},
year = {2012},
date = {2012-01-01},
journal = {Journal of Molecular Modeling},
volume = {19},
number = {7},
pages = {2835--2844},
publisher = {Springer Science and Business Media LLC},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Hernandez2012,
title = {A fragmentation model with neighborhood interaction},
author = {G Hernandez and R Leon and L Salinas and E Dimnet},
url = {https://doi.org/10.1016/j.apm.2011.09.019},
doi = {10.1016/j.apm.2011.09.019},
year = {2012},
date = {2012-01-01},
journal = {Applied Mathematical Modelling},
volume = {36},
number = {4},
pages = {1694--1702},
publisher = {Elsevier BV},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Saldias2012,
title = {One dimensional inorganic oxovanadium polymers functionalized with manganese(II) complexes: Structural and magnetic characterization},
author = {M Saldias and V Paredes-Garcia and A Vega and W Canon-Mancisidor and Le E Fur and D Venegas-Yazigi and E Spodine},
url = {https://doi.org/10.1016/j.poly.2012.04.031},
doi = {10.1016/j.poly.2012.04.031},
year = {2012},
date = {2012-01-01},
journal = {Polyhedron},
volume = {41},
number = {1},
pages = {120--126},
publisher = {Elsevier BV},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Travisany2012,
title = {Draft Genome Sequence of the Sulfobacillus thermosulfidooxidans Cutipay Strain, an Indigenous Bacterium Isolated from a Naturally Extreme Mining Environment in Northern Chile},
author = {D Travisany and Di A Genova and A Sepulveda and R A Bobadilla-Fazzini and P Parada and A Maass},
url = {https://doi.org/10.1128/jb.01622-12},
doi = {10.1128/jb.01622-12},
year = {2012},
date = {2012-01-01},
journal = {Journal of Bacteriology},
volume = {194},
number = {22},
pages = {6327--6328},
publisher = {American Society for Microbiology},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Valle2012,
title = {BINARY-DISK INTERACTION: GAP-OPENING CRITERIA},
author = {Luciano del Valle and Andres Escala},
url = {https://doi.org/10.1088/0004-637x/761/1/31},
doi = {10.1088/0004-637x/761/1/31},
year = {2012},
date = {2012-01-01},
journal = {The Astrophysical Journal},
volume = {761},
number = {1},
pages = {31},
publisher = {IOP Publishing},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{rangarajan_universal_2012,
title = {Universal Meshes: A new paradigm for computing with nonconforming triangulations},
author = {Ramsharan Rangarajan and Adrian J Lew},
url = {http://arxiv.org/abs/1201.4903},
doi = {10.1002/nme},
year = {2012},
date = {2012-01-01},
journal = {Wiley Online Library},
pages = {1--14},
abstract = {We describe a method for discretizing planar C2-regular domains immersed in non-conforming triangulations. The method consists in constructing mappings from triangles in a background mesh to curvilinear ones that conform exactly to the immersed domain. Constructing such a map relies on a novel way of parameterizing the immersed boundary over a collection of nearby edges with its closest point projection. By interpolating the mappings to curvilinear triangles at select points, we recover isoparametric mappings for the immersed domain defined over the background mesh. Indeed, interpolating the constructed mappings just at the vertices of the background mesh yields a fast meshing algorithm that involves only perturbing a few vertices near the boundary. For the discretization of a curved domain to be robust, we have to impose restrictions on the background mesh. Conversely, these restrictions define a family of domains that can be discretized with a given background mesh. We then say that the background mesh is a universal mesh for such a family of domains. The notion of universal meshes is particularly useful in free/moving boundary problems because the same background mesh can serve as the universal mesh for the evolving domain for time intervals that are independent of the time step. Hence it facilitates a framework for finite element calculations over evolving domains while using a fixed background mesh. Furthermore, since the evolving geometry can be approximated with any desired order, numerical solutions can be computed with high-order accuracy. We demonstrate these ideas with various numerical examples.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Pilz2011,
title = {Modelling basin effects on earthquake ground motion in the Santiago de Chile basin by a spectral element code},
author = {Marco Pilz and Stefano Parolai and Marco Stupazzini and Roberto Paolucci and Jochen Zschau},
url = {https://doi.org/10.1111/j.1365-246x.2011.05183.x},
doi = {10.1111/j.1365-246x.2011.05183.x},
year = {2011},
date = {2011-01-01},
journal = {Geophysical Journal International},
volume = {187},
number = {2},
pages = {929--945},
publisher = {Oxford University Press (OUP)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Lagos2011,
title = {Molecular modeling of Trypanosoma cruzi glutamate cysteine ligase and investigation of its interactions with glutathione},
author = {Carlos F Lagos and Raul Araya-Secchi and Pablo Thomas and Tomas Perez-Acle and Ricardo A Tapia and Cristian O Salas},
url = {https://doi.org/10.1007/s00894-011-1224-z},
doi = {10.1007/s00894-011-1224-z},
year = {2011},
date = {2011-01-01},
journal = {Journal of Molecular Modeling},
volume = {18},
number = {5},
pages = {2055--2064},
publisher = {Springer Science and Business Media LLC},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ArayaSecchi2011,
title = {Molecular dynamics study of the archaeal aquaporin AqpM},
author = {Raul Araya-Secchi and JA Garate and David S Holmes and Tomas Perez-Acle},
url = {https://doi.org/10.1186/1471-2164-12-s4-s8},
doi = {10.1186/1471-2164-12-s4-s8},
year = {2011},
date = {2011-01-01},
journal = {BMC Genomics},
volume = {12},
number = {Suppl 4},
pages = {S8},
publisher = {Springer Science and Business Media LLC},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Villanelo2011,
title = {A model for the Escherichia coli FtsB/FtsL/FtsQ cell division complex},
author = {Felipe Villanelo and Alexis Ordenes and Juan Brunet and Rosalba Lagos and Octavio Monasterio},
url = {https://doi.org/10.1186/1472-6807-11-28},
doi = {10.1186/1472-6807-11-28},
year = {2011},
date = {2011-01-01},
journal = {BMC Structural Biology},
volume = {11},
number = {1},
pages = {28},
publisher = {Springer Science and Business Media LLC},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{2011d,
title = {Genome sequence and analysis of the tuber crop potato},
url = {https://doi.org/10.1038/nature10158},
doi = {10.1038/nature10158},
year = {2011},
date = {2011-01-01},
journal = {Nature},
volume = {475},
number = {7355},
pages = {189--195},
publisher = {Springer Science and Business Media LLC},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Katada2009,
title = {Correlation between Bronsted Acid Strength and Local Structure in Zeolites},
author = {Naonobu Katada and Katsuki Suzuki and Takayuki Noda and German Sastre and Miki Niwa},
url = {https://doi.org/10.1021/jp903788n},
doi = {10.1021/jp903788n},
year = {2009},
date = {2009-01-01},
journal = {The Journal of Physical Chemistry C},
volume = {113},
number = {44},
pages = {19208--19217},
publisher = {American Chemical Society (ACS)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Katada2009b,
title = {Correlation between Bronsted Acid Strength and Local Structure in Zeolites},
author = {Naonobu Katada and Katsuki Suzuki and Takayuki Noda and German Sastre and Miki Niwa},
url = {https://doi.org/10.1021/jp903788n},
doi = {10.1021/jp903788n},
year = {2009},
date = {2009-01-01},
journal = {The Journal of Physical Chemistry C},
volume = {113},
number = {44},
pages = {19208--19217},
publisher = {American Chemical Society (ACS)},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{ISI:000584107600001,
title = {The Keto-Enol Tautomerism of Biliverdin in Bacteriophytochrome: Could it
Explain the Bathochromic Shift in the Pfr Form?(dagger)},
author = {Nery Villegas-Escobar and Ricardo A Matute},
doi = {10.1111/php.13341, Early Access Date = NOV 2020},
issn = {0031-8655},
journal = {PHOTOCHEMISTRY AND PHOTOBIOLOGY},
abstract = {Phytochromes are ubiquitous photoreceptors found in plants, eukaryotic
algae, bacteria and fungi. Particularly, when bacteriophytochrome is
irradiated with light, a Z-to-E (photo)isomerization takes place in the
biliverdin chromophore as part of the Pr-to-Pfr conversion. This
photoisomerization is concomitant with a bathochromic shift in the
Q-band. Based on experimental evidence, we studied a possible keto-enol
tautomerization of BV, as an alternative reaction channel after its
photoisomerization. In this contribution, the noncatalyzed and
water-assisted reaction pathways for the lactam-lactim interconversion
through consecutive keto-enol tautomerization of a model BV species were
studied deeply. It was found that in the absence of water molecules, the
proton transfer reaction is unable to take place at normal conditions,
due to large activation energies, and the endothermic formation of
lactim derivatives prevents its occurrence. However, when a water
molecule assists the process by catalyzing the proton transfer reaction,
the activation free energy lowers considerably. The drastic lowering in
the activation energy for the keto-enol tautomerism is due to the
stabilization of the water moiety through hydrogen bonds along the
reaction coordinate. The absorption spectra were computed for all
tautomers. It was found that the UV-visible absorption bands are in
reasonable agreement with the experimental data. Our results suggest
that although the keto-enol equilibrium is likely favoring the lactam
tautomer, the equilibrium could eventually be shifted in favor of the
lactim, as it has been reported to occur in the dark reversion mechanism
of bathy phytochromes.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{doi:10.1021/acs.jpclett.8b02359,
title = {Ab Initio Prediction of Tunneling Relaxation Times and Effective Demagnetization Barriers in Kramers Lanthanide Single-Molecule Magnets},
author = {Daniel Aravena},
url = {https://doi.org/10.1021/acs.jpclett.8b02359},
doi = {10.1021/acs.jpclett.8b02359},
year = {0000},
date = {0000-01-01},
journal = {The Journal of Physical Chemistry Letters},
volume = {0},
number = {0},
pages = {5327-5333},
abstract = {Single-molecule magnets (SMMs) are promising candidates for molecule-based quantum information devices. Their main limitation is their cryogenic operative temperature. To achieve devices performing at higher temperatures, demagnetization mechanisms must be suppressed by chemical tuning. Electronic structure calculations can provide useful information to rationalize SMM behavior, but they do not provide a direct prediction for the key experimental parameters describing magnetic relaxation (i.e., tunneling relaxation time (τQT) and effective demagnetization barrier (Ueff)). In this Letter, a first-principles model is proposed to predict τQT and Ueff for mononuclear, half-integer spin SMMs, allowing direct comparison with experiment. Model accuracy was assessed against experimental data for 18 mononuclear LnIII complexes (15 DyIII and 3 ErIII) and applied to 3 of the current best-performing SMMs, correctly predicting nontrivial relaxation pathways. The model shows that the combination of single-ion anisotropy and spin–spin dipolar coupling can account for the major part of tunneling demagnetization for the studied systems.},
note = {PMID: 30149712},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{doi:10.1021/acscatal.8b01479,
title = {Building Pyridinium Molecular Wires as Axial Ligands for Tuning the Electrocatalytic Activity of Iron Phthalocyanines for the Oxygen Reduction Reaction},
author = {Ana Pizarro and Gabriel Abarca and Cristian Gutiérrez-Cerón and Diego Cortés-Arriagada and Fabiano Bernardi and Cristhian Berrios and Juan F Silva and Marcos C Rezende and José H Zagal and Rubén Oñate and Ingrid Ponce},
url = {https://doi.org/10.1021/acscatal.8b01479},
doi = {10.1021/acscatal.8b01479},
year = {0000},
date = {0000-01-01},
journal = {ACS Catalysis},
volume = {0},
number = {0},
pages = {8406-8419},
abstract = {We have been able to “tune” the electrocatalytic activity of iron phthalocyanine (FePc) and iron hexadodecachlorophthalocyanine (16(Cl)FePc) for the oxygen reduction reaction (ORR) by manipulating the “pull effect” of pyridinium molecules axially bounded to the phthalocyanine complexes (FePcs). These axial ligands play both the role of molecular anchors and also of molecular wires. The axial ligands also affect the reactivity of the Fe metal center in the phthalocyanine. The “pull effect” originates from the positive charge located on the pyridinium core. We have explored the influence of the core positions (Up or Down), in two structural pyridiniums isomers on the activity of FePc and 16(Cl)FePc for the ORR. Of all self-assembled catalysts tested, the highest catalytic activity was exhibited by the Au(111)/Up/FePc system. XPS measurements and DFT calculations showed that it is possible to tailor the FePc–N(pyridiniums) Fe–O2 binding energies, by changing the core positions and affecting the “pull effect” of pyridiniums. This affects directly the catalytic activity of FePcs. The plot of activity as (log I)E versus the calculated Fe–O2 binding energies gives an activity volcano correlation, indicating that an optimum binding energy of O2 with the Fe center provides the highest activity.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{doi:10.1021/acs.jcim.9b00279,
title = {BRUSELAS: HPC generic and customizable software architecture for 3D ligand-based virtual screening of large molecular databases},
author = {Antonio Jesús Banegas-Luna and José Pedro Cerón-Carrasco and Savins Puertas-Martin and Horacio Perez-Sanchez},
url = {https://doi.org/10.1021/acs.jcim.9b00279},
doi = {10.1021/acs.jcim.9b00279},
year = {0000},
date = {0000-01-01},
journal = {Journal of Chemical Information and Modeling},
volume = {0},
number = {ja},
pages = {null},
abstract = {BRUSELAS (Balanced Rapid and Unrestricted Server for Extensive Ligand-Aimed Screening) is a novel, highly efficient web software architecture for 3D shape and pharmacophore searches in off the cuff libraries. A wide panel of shape and pharmacophore similarity algorithms are combined to avoid unbiased results while yielding consensus scoring functions. To evaluate its reliability, BRUSELAS was tested against other similar servers (e.g. USR-VS, SwissSimilarity, ChemMapper) to search for potential antidiabetic drugs. A web tool is developed for users to customize their tasks and is accessible free of any charge or login at http://bio-hpc.ucam.edu/Bruselas. Source code is available on request.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{doi:10.1021/acs.chemmater.9b04021,
title = {Chemical Diversity in Lead-Free, Layered Double Perovskites: A Combined Experimental and Computational Approach},
author = {Brenda Vargas and Raul Torres-Cadena and Diana T Reyes-Castillo and Joelis Rodriguez-Hernandez and Milan Gembicky and Eduardo Menendez-Proupin and Diego Solis-Ibarra},
url = {https://doi.org/10.1021/acs.chemmater.9b04021},
doi = {10.1021/acs.chemmater.9b04021},
year = {0000},
date = {0000-01-01},
journal = {Chemistry of Materials},
volume = {0},
number = {ja},
pages = {null},
abstract = {Akin to the expansion in compositional diversity that halide double perovskites provided to three-dimensional perovskites, layered double perovskites could further expand the diversity of two-dimensional (2D) perovskites; and therefore, they could also enhance the properties or expand the possible applications of such materials. Despite the great promise of halide 2D double perovskites, up to date, there are only four confirmed members of this family of materials. Herein, we explore 90 hypothetical new members of this family materials, by a combined theoretical, computational, and experimental method. The combination of these tactics allowed us to predict several new materials, out of which we experimentally synthesized and characterize five new layered double perovskites, some of which show promising properties for their use in photovoltaics and optoelectronics. Further, our work highlights the vast diversity of compositions, and therefore, of applications that double-layered perovskites have yet to offer.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{doi:10.1021/acs.jpcc.7b11556,
title = {Towards Controlled Morphology of FeCu Nanoparticles: Cu Concentration and Size Effects},
author = {Javier Rojas-Nunez and Rafael I I Gonzalez and Eduardo M Bringa and Sebastian Allende and Pamela Sepúlveda and Nicolás Arancibia-Miranda and Samuel E Baltazar},
url = {https://doi.org/10.1021/acs.jpcc.7b11556},
doi = {10.1021/acs.jpcc.7b11556},
year = {0000},
date = {0000-01-01},
journal = {The Journal of Physical Chemistry C},
volume = {0},
number = {ja},
pages = {null},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{doi:10.1002/ejic.201800339,
title = {Aromaticity of [M3(µ‐X)3X6]0/2‐ (M = Re and Tc},
author = {Rabanal-León Walter and Vásquez-Espinal Alejandro and Yañez Osvaldo and Pino-Rios Ricardo and Arratia-Pérez Ramiro and Alvarez-Thon Luis and Torres-Vega Juan and Tiznado William},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ejic.201800339},
doi = {10.1002/ejic.201800339},
journal = {European Journal of Inorganic Chemistry},
volume = {0},
number = {ja},
abstract = {We present new evidence that supports the aromatic character of the clusters with the formula: [M3(µ‐X)3X6]0/2‐ (M = Re and Tc},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{luis_steric_nodate,
title = {Steric and electronic factors affecting the conformation of bimetallic Cu(I) complexes. Effect of the aliphatic spacer of tetracoordinating Schiff base ligands.},
author = {Lemus Luis and Díaz Daniel E and Llanos Leonel and Arce Pablo and Lorca Romina and Guerrero Juan and Costamagna Juan and Aravena Daniel and Ferraudi Guillermo and Oliver Allen and Lappin Alexander Graham},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/chem.201802290},
doi = {10.1002/chem.201802290},
journal = {Chemistry – A European Journal},
volume = {0},
number = {ja},
abstract = {A family of six homoleptic [CuI(Ln)]2(ClO4)2 and six heteroleptic [CuI(Ln)(PPh3)2]2(ClO4)2 bimetallic complexes, where Ln are bis‐Schiff base ligands with alkyl spacers of variable length (n= 2‐7 ‐CH2‐), were prepared to evaluate the role of the spacer on the formation of helicates or mesocates. In the homoleptic series, spectroscopic and theoretical studies indicate that preferences for a conformation are based on energetic parameters, mainly, the establishment of non‐covalent interactions. The odd‐even nature of the spacers pre‐conditions the superposition of the aromatic rings to allow the juxtaposition necessary for non‐covalent interactions, while the increase of the length reduces the strength of such interactions. Consequently, complexes with even‐spacers of short length were identified as helicates in solution, [CuI(Ln)]22+ (n=2,4). Complexes [CuI(Ln)]22+ (n=3‐7) dissociate in solution to produce the monometallic complexes in equilibrium, [CuI(Ln)]+. The stability of the bimetallic species is discussed in terms of their conformations. The set of heteroleptic complexes was prepared to evaluate the reach of the 'odd‐even rule' in solid, which is based on the 'zig‐zag' arrangements of the spacers. Based on crystallographic information, 'S' and 'C'‐type conformations of Ln are related to even and odd spacers, respectively. This trend is considered in addition to other factors to explain preferences for either a mesocate or helicate conformation in the homoleptic series.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{doi:10.1002/poc.3889,
title = {Investigation about the complexation of trimethylammonium-derived pillar[5]arene with indole and azaindole derivatives},
author = {Rodrigo Montecinos and Fernanda Diaz-Wilson and Alexis Bravo-Sepulveda and Cristian O Salas and Gonzalo Recabarren-Gajardo and Faruk Nome},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/poc.3889},
doi = {10.1002/poc.3889},
journal = {Journal of Physical Organic Chemistry},
volume = {0},
number = {0},
pages = {e3889},
abstract = {Abstract Indoles and azaindoles are very interesting heterocycles found in naturally occurring and synthetic molecules exhibiting several biological activities associated with its physicochemical properties. Here, we report a study about the inclusion complex formation between trimethylammonium-derived pillar[5]arene (P5A) with indole and azaindole derivatives by NMR and molecular dynamics simulations. Our results indicate that indole forms the most stable inclusion complex of the hosts, with its benzene fragment incorporated near to the centre of the cavity. On the other hand, 5-azaindole presents a weaker interaction with P5A, orienting preferentially the pyrrole moiety toward the host cavity. 7-Azaindole switches between two conformations with the pyridine fragment incorporated inside the cavity. Based on these results, we believe these preliminary study of how the guest structure modifies the structure of the inclusion complexes, and the molecular recognition can be further used in the preparation of new functional supramolecular systems including drug delivery systems.},
note = {e3889 POC-17-0270.R1},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{,
title = {[1210.4469] A Rule-based Model of a Hypothetical Zombie Outbreak: Insights on the role of emotional factors during behavioral adaptation of an artificial population},
url = {https://arxiv.org/abs/1210.4469},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{doi:10.1002/mp.13033,
title = {Technical Note: An hybrid parallel implementation for EGSnrc Monte Carlo user codes},
author = {Edgardo Doerner and Paola Caprile},
url = {https://aapm.onlinelibrary.wiley.com/doi/abs/10.1002/mp.13033},
doi = {10.1002/mp.13033},
journal = {Medical Physics},
volume = {45},
number = {8},
pages = {3969-3973},
abstract = {Purpose The purpose of this study was to present a parallel solution for the EGSnrc Monte Carlo code system combining MPI and OpenMP programming models as an alternative to the provided implementation, based on the use of a batch-queueing system (BQS). Methods Relying on a previous implementation based on OpenMP by E. Doerner and P. Caprile [Med. Phys. 44, 6672 (2017)], this work incorporates MPI features to efficiently distribute the simulation on current high-performance computing (HPC) systems. These features are introduced through properly defined macros, which are enabled depending on the compilation flags given by the user. The presented solution was benchmarked using the DOSXYZnrc code for a 6 MV clinical photon beam impinging on an homogeneous water phantom. Results The platform validation against the serial run results confirmed that the introduction of new features does not modify the final dose distribution. The performance tests indicated that the new implementation was able to handle efficiently the workload distribution among the computing units available. Using all the resources available, the hybrid simulation was 10% faster than the MPI only solution and 30% faster than the BQS implementation. Conclusions The hybrid method presented is a viable solution to parallelize MC simulations using the EGSnrc codes in distributed computing systems in an simple and efficient way, taking advantage of the available resources and giving the user the possibility of choosing between different parallelization schemes (only OpenMP/MPI or a combination of both).},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{doi:10.1002/pssb.201800219,
title = {Energetics and Electronic Properties of Interstitial Chlorine in CdTe},
author = {Walter Orellana and Eduardo Menéndez-Proupin and Mauricio A Flores},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pssb.201800219},
doi = {10.1002/pssb.201800219},
journal = {physica status solidi (b)},
volume = {0},
number = {0},
pages = {1800219},
abstract = {The role of interstitial chlorine in the electronic properties of CdTe is addressed by density functional theory calculations including hybrid functionals and large unit cells. The stability and diffusion energy barriers of the impurity are analyzed as a function of the Fermi level position in the band gap. Chlorine is found to be stable in at least five interstitial sites with rather close formation energies, suggesting that they are all probable to be found. In p-type CdTe, the most stable sites are at the center of a CdTe bond and at a split-interstitial configuration, both acting as shallow donors. Whereas in n-type CdTe, it is found at the tetrahedral site surrounded by Cd hosts, acting as a shallow acceptor. We also find that chlorine can induce a deep acceptor level in the bandgap after binding with three Cd host atoms, which can explain the experimentally observed high resistivity in Cl-doped CdTe. The energy barriers for chlorine diffusion in both p-type and n-type CdTe are also discussed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{solar_service-oriented_nodate,
title = {A Service-Oriented Platform for Approximate Bayesian Computation in Population Genetics},
author = {Roberto Solar and Victor Sepulveda and Alonso Inostrosa-Psijas and Oscar Rojas and Veronica Gil-Costa and Mauricio Marin},
url = {https://doi.org/10.1089/cmb.2018.0217},
doi = {10.1089/cmb.2018.0217},
journal = {Journal of Computational Biology},
volume = {0},
number = {0},
pages = {null},
abstract = {Abstract Approximate Bayesian computation (ABC) is a useful technique developed for solving Bayesian inference without explicitly requiring a likelihood function. In population genetics, it is widely used to extract part of the information about the evolutionary history of genetic data. The ABC compares the summary statistics computed on simulated and observed data sets. Typically, a forward-in-time approach is used to simulate the genetic material of a population starting from an initial ancestral population and following the evolution of the individuals by advancing generation by generation under various demographic and genetic forces. This approach is computationally expensive and requires a large number of computations making the use of high-performance computing crucial for decreasing the overall response times. In this work, we propose a fully distributed web service-oriented platform for ABC that is based on forward-in-time simulations. Our proposal is based on a client-server approach. The client enables users to define simulation scenarios. The server enables efficient and scalable population simulations and can be deployed on a distributed cluster of processors or even in the cloud. It is composed of four services: a workload generator, a simulation controller, a simulation results analyzer, and a result builder. The server performs multithread simulations by executing a simulation kernel encapsulated in a proposed libgdrift library. We present and evaluate three different libgdrift library approaches whose algorithms aim to reduce execution times and memory consumption.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{martinez-ledesma_determination_nodate,
title = {Determination of the Signal Fluctuation Threshold of the Temperature-Ion Composition Ambiguity Problem Using Monte Carlo Simulations},
author = {Miguel Martínez-Ledesma and Marcos Andrés Díaz Quezada},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2018JA026217},
doi = {10.1029/2018JA026217},
journal = {Journal of Geophysical Research: Space Physics},
volume = {0},
number = {ja},
abstract = {Abstract Unambiguously estimating the plasma parameters of the ionosphere at altitudes between 130 and 300 km presents a problem for the Incoherent Scatter Radar (ISR). At these ranges, ISR is unable to distinguish between different mixtures of molecular ions (NO+ and O2+) and atomic oxygen ions (O+). Common solutions to this problem are either to employ empirical or theoretical models of the ionosphere, or to add a priori known plasma parameter information obtained from the Plasma Line of the ISR spectrum. Studies have demonstrated that plasma parameters can be unambiguously estimated in almost noiseless scenarios, not commonly feasible during routine monitoring. In this study, we define a theoretical framework to quantify the ambiguity problem and determine the maximum signal fluctuation levels of the ISR signal to unambiguously estimate plasma parameters. We conduct Monte Carlo simulations for different plasma parameters to evaluate the estimation performance of the most commonly used Non-Linear Least Squares optimization algorithm. Results are shown as probability curves of valid convergence and ‘correct’ estimation. We use simulations to quantify the estimation error when using ionospheric models as initial conditions of the optimization algorithm. We also determine the contribution to the estimation process of different combinations of parameters known from the Plasma Line, the particular contribution of each plasma parameter, and the effect of increasing the level of uncertainty of the parameters known a priori. Results suggest that knowing a priori both electron density and electron temperature parameters allows an unambiguous estimation even at high fluctuation levels.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@techreport{cortes_juvenile_nodate,
title = {Juvenile Incarceration and Adult Recidivism},
author = {Tomás Cortés and Nicolás Grau and Jorge Rivera},
url = {http://www.econ.uchile.cl/uploads/publicacion/30a6e9d638bf04b0e6156c4656718ef718a0659f.pdf},
abstract = {Although there is debate about whether juvenile incarceration deters future crime, it is a common practice worldwide. We contribute to this debate by using Chilean data to assess the causal impact of different types of juvenile incarceration on recidivism in young adulthood (18-21 years old). To address the endogeneity issues, we use the quasi random assignment of detention judges as instrumental variable to estimate the effect of pretrial detention, and the quasi random assignment of public attorneys to estimate the effect of any type of incarceration. Considering a standard IV linear model, we find that pretrial detention increases the probability of recidivism by 61 percentage points (pp), and when we define the treatment as any type of incarceration, this impact is equal to 65 pp. When we estimate bivariate probit models-using a novel approach for estimating this model in the context of fixed effects-the impact of pretrial detention and incar-ceration on recidivism are equal to 12 pp and 15 pp, respectively. We also estimate the marginal treatment effect (MTE), finding that the magnitudes of the marginal effects are larger for those individuals with low treatment probabilities. If we use MTE estimates to calculate the average treatment effect (ATE), the impact of pretrial detention on recidivism is equal to 28 pp. If we define the treatment as any type of incarceration, this impact is equal to 36 pp. Finally, we find that an important mechanism behind these impacts is the effect of these different types of incarceration on high school graduation. JEL Codes: K140, I210.},
keywords = {},
pubstate = {published},
tppubtype = {techreport}
}

@article{doi:10.1002/arch.21557,
title = {Structural investigation of selective binding dynamics for the pheromone-binding protein 1 of the grapevine moth, Lobesia botrana},
author = {Herbert Venthur and Juan Machuca and Ricardo Godoy and Rubén Palma-Millanao and Jing-Jiang Zhou and Giovanni Larama and Leonardo Bardehle and Andrés Quiroz and Ricardo Ceballos and Ana Mutis},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/arch.21557},
doi = {10.1002/arch.21557},
journal = {Archives of Insect Biochemistry and Physiology},
volume = {0},
number = {0},
pages = {e21557},
abstract = {Abstract The European grapevine moth, Lobesia botrana (Denis & Schiffermüller), is a serious pest in vineyards in North and South America. Mating disruption techniques have been used to control and monitor L. botrana on the basis of its sexual communication. This needs a well-tuned olfactory system, in which it is believed that pheromone-binding proteins (PBPs) are key players that transport pheromones in the antennae of moths. In this study, the selectivity of a PBP, named as LbotPBP1, was tested by fluorescence binding assays against 11 sex pheromone components and 6 host plant volatiles. In addition, its binding mechanism was predicted on the basis of structural analyses by molecular docking and complex and steered molecular dynamics (SMD). Our results indicate that LbotPBP1 binds selectively to sex pheromone components over certain host plant volatiles, according to both in vitro and in silico tests. Thus, chain length (14 carbon atoms) and functional groups (i.e., alcohol and ester) appear to be key features for stable binding. Likewise, residues such as Phe12, Phe36, and Phe118 could participate in unspecific binding processes, whilst Ser9, Ser56, and Trp114 could participate in the specific recognition and stabilization of sex pheromones instead of host plant volatiles. Moreover, our SMD approach supported 11-dodecenyl acetate as the best ligand for LbotPBP1. Overall, the dynamics simulations, contact frequency analysis and SMD shed light on the binding mechanism of LbotPBP1 and could overcome the imprecision of molecular docking, supporting the in vitro binding assays. Finally, the role of LbotPBP1 in the chemical ecology of L. botrana is discussed.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@inproceedings{Becerrab,
title = {Hydrodynamics in a Polymeric Nanoslit Pore with Graphene and Hexagonal Boron Nitride Wall Coatings: An Atomistic Study},
author = {Diego Becerra},
abstract = {Santa Maria-Design of efficient nanofluidic platforms requires effective reduction of flow resistance within the channel network. With this purpose, 2D-materials can be deposited on polymeric substrates increasing the transport efficiency of water solutions through nanopores. In the present work, we show that significant drag reduction can be achieved in a polyamide nanoslit pore by using graphene and boron nitride as wall coatings. Here, Molecular Dynamics simulations are performed to study water flow through uncoated and coated polyamide nanoslit pores. From atomistic trajectories, we investigate interfacial properties and evaluate the effect that the polymeric matrix has on water structure inside the pores. Furthermore, we compute density and temperature profiles, molecular orientations, friction coefficient and velocity profiles. Using these observables, we analyze the correlation between local water structure, flow enhancement and slip length. Our results indicate that in coated pores the interactions between water molecules and the underlying polyamide substrate have a significant influence on the flow rates. The insights reported in this work may assist the design of strategies to achieve low friction water transport in nanostructured pores. 1 We thank CONICYT scholarship 21181202 and computational support from DTU and NLHPC.},
keywords = {},
pubstate = {published},
tppubtype = {inproceedings}
}

@article{doi:10.1029/2019JC015206,
title = {Tsunami resonance and spatial pattern of natural oscillation modes with multiple resonators},
author = {R Aranguiz and P A Catálan and C Cecioni and G Bellotti and P Henriquez and J González},
url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2019JC015206},
doi = {10.1029/2019JC015206},
journal = {Journal of Geophysical Research: Oceans},
volume = {0},
number = {ja},
abstract = {Abstract Tsunami resonance and coupled oscillation of shelf and bays modes has been reported to be important in tsunami wave amplification. The main objective of this work is to study the spatial pattern of natural oscillation modes and to analyze the influence of several resonators on the coast of the central Chile, which has a complex morphology with several bays, submarine canyons and a wide continental shelf. First, natural oscillation modes were computed by means of modal analysis of local and regional domains. Second, a dense network of tide gauges and pressure sensors was analyzed to obtain background spectra inside bays. Third, tsunami spectra were computed from both tsunami records and numerical simulations. The results show that the use of modal analysis and background and tsunami spectra is effective for identifying natural oscillation modes. In addition, a dense network of tide gauges is useful to validate the spatial pattern of these natural modes. It was observed that larger resonators and the shelf are important in coupling oscillation with local bays, such that large amplification can be observed. Finally, this analysis allowed the diverse effects of 2010 and 2011 tsunamis in the bays of central Chile to be explained, making it possible to better address tsunami mitigation measures and the preparedness of coastal communities.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@thesis{orfanoz_cheuquelaf_estratificacion_2016,
title = {Estratificación vertical y transporte viento abajo de contaminantes urbanos de Santiago de Chile},
author = {Andrea Paz Orfanoz Cheuquelaf},
url = {http://repositorio.uchile.cl/handle/2250/139755},
institution = {Universidad de Chile},
abstract = {La cuenca de Santiago se ubica en la zona central de Chile, cuenta con una población de alrededor de 7 millones de personas y presenta un relieve complejo caracterizado por cadenas montañosas que rodean la ciudad. Tiene un clima semiárido, una tropósfera baja estable y una inversión térmica de subsidencia cuasi permanente. Todos estos factores, junto a las altas emisiones de la ciudad (6.5 [kton/a] de P M10 y 5.9 [kton/a] de P M2 ,5), favorecen la ocurrencia de altas concentraciones de contaminantes con efectos nocivos sobre la salud de las personas, los ecosistemas y, potencialmente, el clima regional. Varios estudios y caracterizaciones han sido realizados en la zona acerca de la contami- nación atmosférica, particularmente de los tipos de contaminantes y sus fuentes pero no se ha enfatizado en la dinámica de la distribución vertical de los contaminantes o su alcance espacial y temporal. Este trabajo es la primera comparación sistemática de los resultados de un modelo con observaciones verticales de una traza contaminante. Se describe la estratifi- cación vertical y los mecanismos de transporte que afectan a los contaminantes urbanos de Santiago, también se estudia el posible transporte de estos hacia la Cordillera de los Andes. Se utiliza un modelo numérico que simula las condiciones meteorológicas de la cuenca y que utiliza el monóxido de carbono como trazador cuasi-pasivo de contaminantes urbanos. Estas simulaciones se contrastan con observaciones en la vertical de carbono negro durante una campaña de mediciones de 4 días. El modelo reproduce correctamente la condición sinóptica del período, simulando el desa- rrollo de una baja costera intensa. A escala subsinóptica reproduce la circulación entre el valle y la montaña, característica de Santiago. Tanto las simulaciones como las observaciones muestran la presencia de capas elevadas de contaminantes, las que, sugiere el modelo, son producto de una recirculación de contaminantes emitidos en Santiago. Las simulaciones muestran el transporte de contaminantes hacia la zona andina, alcanzan- do lugares por sobre los 4000 metros de altitud. El mecanismo de transporte hacia la cordillera exhibido por las simulaciones está asociado a la circulación termal de valle y montaña.},
keywords = {},
pubstate = {published},
tppubtype = {thesis}
}

@thesis{teneb_lobos_diseno_2016b,
title = {Diseño de un Ligando Peptídico con Afinidad por la Hormona Folículo Estimulante Humana Tesis para optar al grado de Magíster en Bioquímica y Bioinformática},
author = {Jaime Camilo Teneb Lobos},
url = {http://repositorio.udec.cl/bitstream/handle/11594/2045/TESIS_MAGISTER_JT.pdf},
institution = {Universidad de Concepción},
abstract = {La Hormona Folículo Estimulante (FSH) es una glicoproteína que está involucrada en el desarrollo sexual y la función reproductiva en vertebrados. Debido a esto, es utilizada como agente terapéutico para casos de infertilidad de origen femenino desde principio de la década del 60 y posteriormente, también se incorporó en casos de infertilidad de origen masculino. Comercialmente, los fármacos basados en FSH registran ventas de $1.30 billones de dólares durante el 2013 con un 2% de aumento con respecto al año anterior, presentándose en décimo tercer lugar de las familias de biofármacos más vendidos en el mundo. La principal preparación de FSH humana en la actualidad es Gonal-f con dos tercios del mercado; en conjunto con otros preparados poseen un proceso de purificación basado en cromatografía de afinidad que utiliza anticuerpos monoclonales. La cromatografía de afinidad es un método de separación basado en la propiedad de las moléculas biológicas, principalmente anticuerpos, de unir ligandos específicamente por complementariedad de superficies y fuerzas intermoleculares. A pesar de que el uso de anticuerpos ha demostrado ser muy eficaz en cromatografía de afinidad, actualmente existe una tendencia a reemplazar el uso de anticuerpos por ligandos peptídicos pequeños que poseen especificidad y afinidad similar a los anticuerpos, pero presentan una mayor estabilidad y menor costo de producción. En este trabajo se busca diseñar un ligando peptídico que presente alta afinidad por la FSH humana y pueda ser utilizado en un proceso de purificación por cromatografía de afinidad. Para realizar el diseño del péptido, nos hemos basado en el análisis de interfaz proteínaproteína del complejo FSH-FSHR. Se encontró un grupo de residuos con cercanía lineal, conformado por el residuo modificado de tirosina sulfatada sTyr335 y Leu337, que poseen una gran parte de su superficie internalizada en el complejo, y con un cambio de energía de unión (textbackslashDeltatextbackslashDeltaG) significativo, identificado por barrido de alanina in silico, suficientes para ser considerados hotspots. Cercano a estos residuos, existe una zona de estructura indeterminada en el receptor. Con el objetivo de analizar el aporte de los residuos de este lazo en la interacción del complejo, se generó un modelo del exodominio del receptor completo, y así, realizar una simulación de dinámica molecular del complejo por un tiempo de 50 ns, para estudiar su comportamiento en un sistema termodinámico completo. Del análisis de dinámica en estructuras de menor energía, se encontró que el residuo M328, del lazo de estructura desconocida, presenta una superficie internalizada en el complejo considerable, y un textbackslashDeltatextbackslashDeltaG que nos lleva a considerarlo hotspot. De esta forma encontramos una secuencia de 10 residuos que posee 3 hotspots. Posteriormente, basados en esta secuencia, diseñamos un péptido para utilización en una matriz de purificación de sefarosa N-Hidroxisuccinamida para cromatografía de afinidad y evaluamos la energía de unión del complejo FSH-péptido por MM/PBSA. El valor predictivo de textbackslashDeltaGunión es -15,4 ± 6,9 kcal/mol lo que sugiere que el péptido diseñado en este trabajo tiene potencial para ser utilizado en la purificación de FSH humana.},
keywords = {},
pubstate = {published},
tppubtype = {thesis}
}

@thesis{orfanoz_cheuquelaf_estratificacion_2016b,
title = {Estratificación vertical y transporte viento abajo de contaminantes urbanos de Santiago de Chile},
author = {Andrea Paz Orfanoz Cheuquelaf},
url = {http://repositorio.uchile.cl/handle/2250/139755},
institution = {Universidad de Chile},
abstract = {La cuenca de Santiago se ubica en la zona central de Chile, cuenta con una población de alrededor de 7 millones de personas y presenta un relieve complejo caracterizado por cadenas montañosas que rodean la ciudad. Tiene un clima semiárido, una tropósfera baja estable y una inversión térmica de subsidencia cuasi permanente. Todos estos factores, junto a las altas emisiones de la ciudad (6.5 [kton/a] de P M10 y 5.9 [kton/a] de P M2 ,5), favorecen la ocurrencia de altas concentraciones de contaminantes con efectos nocivos sobre la salud de las personas, los ecosistemas y, potencialmente, el clima regional. Varios estudios y caracterizaciones han sido realizados en la zona acerca de la contami- nación atmosférica, particularmente de los tipos de contaminantes y sus fuentes pero no se ha enfatizado en la dinámica de la distribución vertical de los contaminantes o su alcance espacial y temporal. Este trabajo es la primera comparación sistemática de los resultados de un modelo con observaciones verticales de una traza contaminante. Se describe la estratifi- cación vertical y los mecanismos de transporte que afectan a los contaminantes urbanos de Santiago, también se estudia el posible transporte de estos hacia la Cordillera de los Andes. Se utiliza un modelo numérico que simula las condiciones meteorológicas de la cuenca y que utiliza el monóxido de carbono como trazador cuasi-pasivo de contaminantes urbanos. Estas simulaciones se contrastan con observaciones en la vertical de carbono negro durante una campaña de mediciones de 4 días. El modelo reproduce correctamente la condición sinóptica del período, simulando el desa- rrollo de una baja costera intensa. A escala subsinóptica reproduce la circulación entre el valle y la montaña, característica de Santiago. Tanto las simulaciones como las observaciones muestran la presencia de capas elevadas de contaminantes, las que, sugiere el modelo, son producto de una recirculación de contaminantes emitidos en Santiago. Las simulaciones muestran el transporte de contaminantes hacia la zona andina, alcanzan- do lugares por sobre los 4000 metros de altitud. El mecanismo de transporte hacia la cordillera exhibido por las simulaciones está asociado a la circulación termal de valle y montaña.},
keywords = {},
pubstate = {published},
tppubtype = {thesis}
}

@thesis{teneb_lobos_diseno_2016b,
title = {Diseño de un Ligando Peptídico con Afinidad por la Hormona Folículo Estimulante Humana Tesis para optar al grado de Magíster en Bioquímica y Bioinformática},
author = {Jaime Camilo Teneb Lobos},
institution = {Universidad de Concepción},
abstract = {La Hormona Folículo Estimulante (FSH) es una glicoproteína que está involucrada en el desarrollo sexual y la función reproductiva en vertebrados. Debido a esto, es utilizada como agente terapéutico para casos de infertilidad de origen femenino desde principio de la década del 60 y posteriormente, también se incorporó en casos de infertilidad de origen masculino. Comercialmente, los fármacos basados en FSH registran ventas de $1.30 billones de dólares durante el 2013 con un 2% de aumento con respecto al año anterior, presentándose en décimo tercer lugar de las familias de biofármacos más vendidos en el mundo. La principal preparación de FSH humana en la actualidad es Gonal-f con dos tercios del mercado; en conjunto con otros preparados poseen un proceso de purificación basado en cromatografía de afinidad que utiliza anticuerpos monoclonales. La cromatografía de afinidad es un método de separación basado en la propiedad de las moléculas biológicas, principalmente anticuerpos, de unir ligandos específicamente por complementariedad de superficies y fuerzas intermoleculares. A pesar de que el uso de anticuerpos ha demostrado ser muy eficaz en cromatografía de afinidad, actualmente existe una tendencia a reemplazar el uso de anticuerpos por ligandos peptídicos pequeños que poseen especificidad y afinidad similar a los anticuerpos, pero presentan una mayor estabilidad y menor costo de producción. En este trabajo se busca diseñar un ligando peptídico que presente alta afinidad por la FSH humana y pueda ser utilizado en un proceso de purificación por cromatografía de afinidad. Para realizar el diseño del péptido, nos hemos basado en el análisis de interfaz proteínaproteína del complejo FSH-FSHR. Se encontró un grupo de residuos con cercanía lineal, conformado por el residuo modificado de tirosina sulfatada sTyr335 y Leu337, que poseen una gran parte de su superficie internalizada en el complejo, y con un cambio de energía de unión (textbackslashDeltatextbackslashDeltaG) significativo, identificado por barrido de alanina in silico, suficientes para ser considerados hotspots. Cercano a estos residuos, existe una zona de estructura indeterminada en el receptor. Con el objetivo de analizar el aporte de los residuos de este lazo en la interacción del complejo, se generó un modelo del exodominio del receptor completo, y así, realizar una simulación de dinámica molecular del complejo por un tiempo de 50 ns, para estudiar su comportamiento en un sistema termodinámico completo. Del análisis de dinámica en estructuras de menor energía, se encontró que el residuo M328, del lazo de estructura desconocida, presenta una superficie internalizada en el complejo considerable, y un textbackslashDeltatextbackslashDeltaG que nos lleva a considerarlo hotspot. De esta forma encontramos una secuencia de 10 residuos que posee 3 hotspots. Posteriormente, basados en esta secuencia, diseñamos un péptido para utilización en una matriz de purificación de sefarosa N-Hidroxisuccinamida para cromatografía de afinidad y evaluamos la energía de unión del complejo FSH-péptido por MM/PBSA. El valor predictivo de textbackslashDeltaGunión es -15,4 ± 6,9 kcal/mol lo que sugiere que el péptido diseñado en este trabajo tiene potencial para ser utilizado en la purificación de FSH humana.},
keywords = {},
pubstate = {published},
tppubtype = {thesis}
}

@thesis{teneb_lobos_diseno_2016-1,
title = {Diseño de un Ligando Peptídico con Afinidad por la Hormona Folículo Estimulante Humana Tesis para optar al grado de Magíster en Bioquímica y Bioinformática},
author = {Jaime Camilo Teneb Lobos},
url = {http://repositorio.udec.cl/bitstream/handle/11594/2045/TESIS_MAGISTER_JT.pdf},
institution = {Universidad de Concepción},
abstract = {La Hormona Folículo Estimulante (FSH) es una glicoproteína que está involucrada en el desarrollo sexual y la función reproductiva en vertebrados. Debido a esto, es utilizada como agente terapéutico para casos de infertilidad de origen femenino desde principio de la década del 60 y posteriormente, también se incorporó en casos de infertilidad de origen masculino. Comercialmente, los fármacos basados en FSH registran ventas de $1.30 billones de dólares durante el 2013 con un 2% de aumento con respecto al año anterior, presentándose en décimo tercer lugar de las familias de biofármacos más vendidos en el mundo. La principal preparación de FSH humana en la actualidad es Gonal-f con dos tercios del mercado; en conjunto con otros preparados poseen un proceso de purificación basado en cromatografía de afinidad que utiliza anticuerpos monoclonales. La cromatografía de afinidad es un método de separación basado en la propiedad de las moléculas biológicas, principalmente anticuerpos, de unir ligandos específicamente por complementariedad de superficies y fuerzas intermoleculares. A pesar de que el uso de anticuerpos ha demostrado ser muy eficaz en cromatografía de afinidad, actualmente existe una tendencia a reemplazar el uso de anticuerpos por ligandos peptídicos pequeños que poseen especificidad y afinidad similar a los anticuerpos, pero presentan una mayor estabilidad y menor costo de producción. En este trabajo se busca diseñar un ligando peptídico que presente alta afinidad por la FSH humana y pueda ser utilizado en un proceso de purificación por cromatografía de afinidad. Para realizar el diseño del péptido, nos hemos basado en el análisis de interfaz proteínaproteína del complejo FSH-FSHR. Se encontró un grupo de residuos con cercanía lineal, conformado por el residuo modificado de tirosina sulfatada sTyr335 y Leu337, que poseen una gran parte de su superficie internalizada en el complejo, y con un cambio de energía de unión (textbackslashDeltatextbackslashDeltaG) significativo, identificado por barrido de alanina in silico, suficientes para ser considerados hotspots. Cercano a estos residuos, existe una zona de estructura indeterminada en el receptor. Con el objetivo de analizar el aporte de los residuos de este lazo en la interacción del complejo, se generó un modelo del exodominio del receptor completo, y así, realizar una simulación de dinámica molecular del complejo por un tiempo de 50 ns, para estudiar su comportamiento en un sistema termodinámico completo. Del análisis de dinámica en estructuras de menor energía, se encontró que el residuo M328, del lazo de estructura desconocida, presenta una superficie internalizada en el complejo considerable, y un textbackslashDeltatextbackslashDeltaG que nos lleva a considerarlo hotspot. De esta forma encontramos una secuencia de 10 residuos que posee 3 hotspots. Posteriormente, basados en esta secuencia, diseñamos un péptido para utilización en una matriz de purificación de sefarosa N-Hidroxisuccinamida para cromatografía de afinidad y evaluamos la energía de unión del complejo FSH-péptido por MM/PBSA. El valor predictivo de textbackslashDeltaGunión es -15,4 ± 6,9 kcal/mol lo que sugiere que el péptido diseñado en este trabajo tiene potencial para ser utilizado en la purificación de FSH humana.},
keywords = {},
pubstate = {published},
tppubtype = {thesis}
}

@article{berlanga_formation_2017-1b,
title = {Formation of self-assembled monolayer of curcuminoid molecules on gold surfaces},
author = {Isadora Berlanga and Álvaro Etcheverry-Berríos and Andy Mella and Domingo Jullian and Victoria Alejandra Gómez and Núria Aliaga-Alcalde and Victor Fuenzalida and Marcos Flores and Monica Soler},
url = {http://dx.doi.org/doi:10.1016/j.apsusc.2016.09.077},
doi = {10.1016/j.apsusc.2016.09.077},
issn = {01694332},
volume = {392},
pages = {834--840},
abstract = {We investigated the formation of self-assembled monolayers of two thiophene curcuminoid molecules, 2-thphCCM (1) and 3-thphCCM (2), on polycrystalline gold substrates prepared by immersion of the surfaces in a solution of the molecules during 24 h. The functionalized surfaces were studied by scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS). Despite the fact that both molecules have the same composition and almost the same structure, these molecules exhibit different behavior on the gold surface, which can be explained by the different positions of the sulfur atoms in the terminal aromatic rings. In the case of molecule 1, the complete formation of a SAM can be observed after 24 h of immersion. In the case of molecule 2, the transition from flat-lying to upright configuration on the surface is still in process after 24 h of immersion. This is attributed to the fact that molecule 2 have the sulfur atoms more exposed than molecule 1.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@thesis{orfanoz_cheuquelaf_estratificacion_2016bb,
title = {Estratificación vertical y transporte viento abajo de contaminantes urbanos de Santiago de Chile},
author = {Andrea Paz Orfanoz Cheuquelaf},
url = {http://repositorio.uchile.cl/handle/2250/139755},
institution = {Universidad de Chile},
abstract = {La cuenca de Santiago se ubica en la zona central de Chile, cuenta con una población de alrededor de 7 millones de personas y presenta un relieve complejo caracterizado por cadenas montañosas que rodean la ciudad. Tiene un clima semiárido, una tropósfera baja estable y una inversión térmica de subsidencia cuasi permanente. Todos estos factores, junto a las altas emisiones de la ciudad (6.5 [kton/a] de P M10 y 5.9 [kton/a] de P M2 ,5), favorecen la ocurrencia de altas concentraciones de contaminantes con efectos nocivos sobre la salud de las personas, los ecosistemas y, potencialmente, el clima regional. Varios estudios y caracterizaciones han sido realizados en la zona acerca de la contami- nación atmosférica, particularmente de los tipos de contaminantes y sus fuentes pero no se ha enfatizado en la dinámica de la distribución vertical de los contaminantes o su alcance espacial y temporal. Este trabajo es la primera comparación sistemática de los resultados de un modelo con observaciones verticales de una traza contaminante. Se describe la estratifi- cación vertical y los mecanismos de transporte que afectan a los contaminantes urbanos de Santiago, también se estudia el posible transporte de estos hacia la Cordillera de los Andes. Se utiliza un modelo numérico que simula las condiciones meteorológicas de la cuenca y que utiliza el monóxido de carbono como trazador cuasi-pasivo de contaminantes urbanos. Estas simulaciones se contrastan con observaciones en la vertical de carbono negro durante una campaña de mediciones de 4 días. El modelo reproduce correctamente la condición sinóptica del período, simulando el desa- rrollo de una baja costera intensa. A escala subsinóptica reproduce la circulación entre el valle y la montaña, característica de Santiago. Tanto las simulaciones como las observaciones muestran la presencia de capas elevadas de contaminantes, las que, sugiere el modelo, son producto de una recirculación de contaminantes emitidos en Santiago. Las simulaciones muestran el transporte de contaminantes hacia la zona andina, alcanzan- do lugares por sobre los 4000 metros de altitud. El mecanismo de transporte hacia la cordillera exhibido por las simulaciones está asociado a la circulación termal de valle y montaña.},
keywords = {},
pubstate = {published},
tppubtype = {thesis}
}

@thesis{teneb_lobos_diseno_2016bc,
title = {Diseño de un Ligando Peptídico con Afinidad por la Hormona Folículo Estimulante Humana Tesis para optar al grado de Magíster en Bioquímica y Bioinformática},
author = {Jaime Camilo Teneb Lobos},
institution = {Universidad de Concepción},
abstract = {La Hormona Folículo Estimulante (FSH) es una glicoproteína que está involucrada en el desarrollo sexual y la función reproductiva en vertebrados. Debido a esto, es utilizada como agente terapéutico para casos de infertilidad de origen femenino desde principio de la década del 60 y posteriormente, también se incorporó en casos de infertilidad de origen masculino. Comercialmente, los fármacos basados en FSH registran ventas de $1.30 billones de dólares durante el 2013 con un 2% de aumento con respecto al año anterior, presentándose en décimo tercer lugar de las familias de biofármacos más vendidos en el mundo. La principal preparación de FSH humana en la actualidad es Gonal-f con dos tercios del mercado; en conjunto con otros preparados poseen un proceso de purificación basado en cromatografía de afinidad que utiliza anticuerpos monoclonales. La cromatografía de afinidad es un método de separación basado en la propiedad de las moléculas biológicas, principalmente anticuerpos, de unir ligandos específicamente por complementariedad de superficies y fuerzas intermoleculares. A pesar de que el uso de anticuerpos ha demostrado ser muy eficaz en cromatografía de afinidad, actualmente existe una tendencia a reemplazar el uso de anticuerpos por ligandos peptídicos pequeños que poseen especificidad y afinidad similar a los anticuerpos, pero presentan una mayor estabilidad y menor costo de producción. En este trabajo se busca diseñar un ligando peptídico que presente alta afinidad por la FSH humana y pueda ser utilizado en un proceso de purificación por cromatografía de afinidad. Para realizar el diseño del péptido, nos hemos basado en el análisis de interfaz proteínaproteína del complejo FSH-FSHR. Se encontró un grupo de residuos con cercanía lineal, conformado por el residuo modificado de tirosina sulfatada sTyr335 y Leu337, que poseen una gran parte de su superficie internalizada en el complejo, y con un cambio de energía de unión (textbackslashDeltatextbackslashDeltaG) significativo, identificado por barrido de alanina in silico, suficientes para ser considerados hotspots. Cercano a estos residuos, existe una zona de estructura indeterminada en el receptor. Con el objetivo de analizar el aporte de los residuos de este lazo en la interacción del complejo, se generó un modelo del exodominio del receptor completo, y así, realizar una simulación de dinámica molecular del complejo por un tiempo de 50 ns, para estudiar su comportamiento en un sistema termodinámico completo. Del análisis de dinámica en estructuras de menor energía, se encontró que el residuo M328, del lazo de estructura desconocida, presenta una superficie internalizada en el complejo considerable, y un textbackslashDeltatextbackslashDeltaG que nos lleva a considerarlo hotspot. De esta forma encontramos una secuencia de 10 residuos que posee 3 hotspots. Posteriormente, basados en esta secuencia, diseñamos un péptido para utilización en una matriz de purificación de sefarosa N-Hidroxisuccinamida para cromatografía de afinidad y evaluamos la energía de unión del complejo FSH-péptido por MM/PBSA. El valor predictivo de textbackslashDeltaGunión es -15,4 ± 6,9 kcal/mol lo que sugiere que el péptido diseñado en este trabajo tiene potencial para ser utilizado en la purificación de FSH humana.},
keywords = {},
pubstate = {published},
tppubtype = {thesis}
}

@thesis{teneb_lobos_diseno_2016-1b,
title = {Diseño de un Ligando Peptídico con Afinidad por la Hormona Folículo Estimulante Humana Tesis para optar al grado de Magíster en Bioquímica y Bioinformática},
author = {Jaime Camilo Teneb Lobos},
url = {http://repositorio.udec.cl/bitstream/handle/11594/2045/TESIS_MAGISTER_JT.pdf},
institution = {Universidad de Concepción},
abstract = {La Hormona Folículo Estimulante (FSH) es una glicoproteína que está involucrada en el desarrollo sexual y la función reproductiva en vertebrados. Debido a esto, es utilizada como agente terapéutico para casos de infertilidad de origen femenino desde principio de la década del 60 y posteriormente, también se incorporó en casos de infertilidad de origen masculino. Comercialmente, los fármacos basados en FSH registran ventas de $1.30 billones de dólares durante el 2013 con un 2% de aumento con respecto al año anterior, presentándose en décimo tercer lugar de las familias de biofármacos más vendidos en el mundo. La principal preparación de FSH humana en la actualidad es Gonal-f con dos tercios del mercado; en conjunto con otros preparados poseen un proceso de purificación basado en cromatografía de afinidad que utiliza anticuerpos monoclonales. La cromatografía de afinidad es un método de separación basado en la propiedad de las moléculas biológicas, principalmente anticuerpos, de unir ligandos específicamente por complementariedad de superficies y fuerzas intermoleculares. A pesar de que el uso de anticuerpos ha demostrado ser muy eficaz en cromatografía de afinidad, actualmente existe una tendencia a reemplazar el uso de anticuerpos por ligandos peptídicos pequeños que poseen especificidad y afinidad similar a los anticuerpos, pero presentan una mayor estabilidad y menor costo de producción. En este trabajo se busca diseñar un ligando peptídico que presente alta afinidad por la FSH humana y pueda ser utilizado en un proceso de purificación por cromatografía de afinidad. Para realizar el diseño del péptido, nos hemos basado en el análisis de interfaz proteínaproteína del complejo FSH-FSHR. Se encontró un grupo de residuos con cercanía lineal, conformado por el residuo modificado de tirosina sulfatada sTyr335 y Leu337, que poseen una gran parte de su superficie internalizada en el complejo, y con un cambio de energía de unión (textbackslashDeltatextbackslashDeltaG) significativo, identificado por barrido de alanina in silico, suficientes para ser considerados hotspots. Cercano a estos residuos, existe una zona de estructura indeterminada en el receptor. Con el objetivo de analizar el aporte de los residuos de este lazo en la interacción del complejo, se generó un modelo del exodominio del receptor completo, y así, realizar una simulación de dinámica molecular del complejo por un tiempo de 50 ns, para estudiar su comportamiento en un sistema termodinámico completo. Del análisis de dinámica en estructuras de menor energía, se encontró que el residuo M328, del lazo de estructura desconocida, presenta una superficie internalizada en el complejo considerable, y un textbackslashDeltatextbackslashDeltaG que nos lleva a considerarlo hotspot. De esta forma encontramos una secuencia de 10 residuos que posee 3 hotspots. Posteriormente, basados en esta secuencia, diseñamos un péptido para utilización en una matriz de purificación de sefarosa N-Hidroxisuccinamida para cromatografía de afinidad y evaluamos la energía de unión del complejo FSH-péptido por MM/PBSA. El valor predictivo de textbackslashDeltaGunión es -15,4 ± 6,9 kcal/mol lo que sugiere que el péptido diseñado en este trabajo tiene potencial para ser utilizado en la purificación de FSH humana.},
keywords = {},
pubstate = {published},
tppubtype = {thesis}
}

@article{siddikov_gpds_2017b,
title = {GPDs from charged current meson production in $ep$ experiments},
author = {Marat Siddikov and Ivan Schmidt},
url = {http://arxiv.org/abs/1709.01405},
pages = {15},
abstract = {We suggest that generalized parton distributions can be probed in charged current meson production process, $eptextbackslashbackslashtotextbackslashbackslashnu_etextbackslashbackslashpitextasciicircum-p$. In contrast to pion photoproduction, this process is sensitive to the unpolarized GPDs $H,textbackslashbackslash,E$, and for this reason has a very small contamination by higher twist and Bethe-Heitler type contributions. Since all produced hadrons are charged, we expect that the kinematics of this process could be easily reconstructed. We estimated the cross-sections in the kinematics of upgraded 12 GeV Jefferson Laboratory experiments and found that thanks to large luminosity the process can be measured with reasonable statistics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{perez-sanchez_implementation_2017,
title = {Implementation of an Efficient Blind Docking Technique on HPC Architectures for the Discovery of Allosteric Inhibitors},
author = {Horacio Perez-Sanchez and Jose P Ceron-Carrasco and Jose M Cecilia},
url = {http://ieeexplore.ieee.org/document/8026066/},
doi = {10.1109/ICPPW.2017.18},
pages = {33--38},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{flores_adsorption_2017,
title = {Adsorption of 2-thiophene curcuminoid molecules on a Au(111) surface},
author = {M Flores and E Cisternas and A Mella and D Julian and A S Nunez and M Soler},
url = {http://linkinghub.elsevier.com/retrieve/pii/S0169433217325345},
doi = {10.1016/j.apsusc.2017.08.211},
issn = {01694332},
number = {111},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{robinson_duggon_supramolecular_2017,
title = {Supramolecular Reversible On-Off Switch for Singlet Oxygen Using Cucurbit[n]uril Inclusion Complexes},
author = {José Robinson Duggon and Francisco Pérez Mora and Liliana Valverde Vásquez and Diego Cortés Arriagada and Julio Ramón De la Fuente and Germán Günther and Denis Fuentealba},
url = {http://pubs.acs.org/doi/abs/10.1021/acs.jpcc.7b07736},
doi = {10.1021/acs.jpcc.7b07736},
issn = {1932-7447},
pages = {9},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{barrientos_gpu-based_2017,
title = {GPU-based exhaustive algorithms processing kNN queries},
author = {Ricardo J Barrientos and Fabricio Millaguir and José L Sánchez and Enrique Arias},
url = {http://link.springer.com/10.1007/s11227-017-2110-y},
doi = {10.1007/s11227-017-2110-y},
issn = {0920-8542},
volume = {73},
number = {10},
pages = {4611--4634},
abstract = {Efficient kNN search, or k-nearest neighbors search, is useful, among other fields, in multimedia information retrieval, data mining and pattern recognition problems. A distance function determines how similar the objects are to a given kNN query object. As finding the distance between any given pair of objects (i.e., high-dimensional vectors) is known to be a computationally expensive operation, using parallel computation techniques is an effective way of reducing running times to acceptable values in large databases. In the present work, we offer novel GPU approaches to solving kNN (k-nearest neighbor) queries using exhaustive algorithms based on the Selection Sort, Quicksort and state-of-the-art algorithms. We show that the best approach depends on the k value of the kNN query and achieve a speedup up to 86.4× better than the sequential counterpart. We also propose a multi-core algorithm to be used as reference for the experiments and a hybrid algorithm which combines the proposed algorithms with a state-of-the-art heaps-based method, in which the best performance is obtained with high k values. We also extend our algorithms to be able to deal with large databases that do not fit in GPU memory and whose performance does not deteriorate as database size increases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{peralta_vibrational_2017,
title = {Vibrational properties of Cu3XY4 sulvanites (X = Nb, Ta, and V; and Y = S, and Se) by ab initio molecular dynamics},
author = {Joaquín Peralta and Camilo Valencia Balvín},
url = {http://link.springer.com/10.1140/epjb/e2017-80050-7},
doi = {10.1140/epjb/e2017-80050-7},
issn = {1434-6028},
volume = {90},
number = {9},
pages = {177},
abstract = {In this work, we present a structural and dynamic characterisation of six different types of sulvanites Cu 3 XY 4 with X = Nb, V and Ta, and Y = S and Se. These materials have been the subject of intense study in recent times primarily as potential candidates for solar cell devices, as well as for their enhanced opto-electrical properties. Here, by means of first-principles calculations, we study the structural and dynamic behaviour of these materials at different temperatures, which is important for use of these materials in high-temperature conditions. In this work the dynamic and structural properties are studied using the Density Functional Theory technique. The simulations were performed at four different temperatures, ranging from room temperature to ∼ 1500 K. By using first-principles molecular dynamics in the microcanonical ensemble, we are able to determine the vibrational spectra of these sulvanites. With this information we report for the first time the partial vibrational density of states of these structures at different temperatures. With these results we determine the vibrational properties of the basic building blocks of those sulvanites and their dynamic behaviour under temperature effects. We also show that the building blocks that which make up these structures, remain stable as the temperature increases.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{rabanal-le_exploring_nodate,
title = {Exploring the potential energy surface of small lead clusters using the gradient embedded genetic algorithm and an adequate treatment of relativistic effects},
author = {Walter A Rabanal-Lé and William Tiznado and Edison Osorio and Franklin Ferraro},
doi = {10.1039/c7ra11449d},
abstract = {It is a well-known fact that theoretical methodologies play a crucial role to assure an adequate structural assignment of gas-phase clusters. Particularly, in heavy-element containing clusters the inclusion of relativistic effects (scalar and spin–orbit coupling) can significantly affect their chemistry. Therefore, these effects become the keystone on their structural determination. In our work, the way in which relativistic effects were treated, as well as their influence in the process of an adequate identification of lowest-energy isomer (the global minima – " GM " – energy structure), were evaluated in small lead clusters. The potential energy surfaces of small Pb n (n ¼ 3–10) clusters was explored by means of the gradient embedded genetic algorithm program (GEGA). Subsequently, the most stable isomers were re-optimized incorporating relativistic effects through two different approximations: (i) using relativistic effective core potentials (RECPs) or pseudopotentials, which mimics the scalar and spin–orbit coupling relativistic effects (SR and SO) of the core electrons; and (ii) using relativistic Hamiltonians (with proper all-electron basis sets), like, the zeroth-order regular approximation (ZORA) to the Dirac equation, in which the scalar (SR) and spin–orbit coupling (SOC) relativistic effects were also included. The results evidence that methodologies including SOC effect allow to identify the GM energy structure correctly in all the studied cases. Besides, the GEGA algorithm, using a modest RECP, provides good initial structures that become GM after re-optimization at the SOC level.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}