Publications that acknowledge the role of the NLHPC in their research
2019 |
Bernales, Maricarmen; Monsalve, Liliam; Ayala-Raso, Anibal; Valdenegro, Monika; Martínez, Juan-Pablo; Travisany, Dante; Defilippi, Bruno; González-Agüero, Mauricio; Cherian, Sam; Fuentes, Lida Expression of two indole-3-acetic acid (IAA)-amido synthetase (GH3) genes during fruit development of raspberry (Rubus idaeus Heritage) Journal Article Scientia Horticulturae, 246 , pp. 168 – 175, 2019, ISSN: 0304-4238. @article{bernales_expression_2019, title = {Expression of two indole-3-acetic acid (IAA)-amido synthetase (GH3) genes during fruit development of raspberry (Rubus idaeus Heritage)}, author = {Maricarmen Bernales and Liliam Monsalve and Anibal Ayala-Raso and Monika Valdenegro and Juan-Pablo Mart\'{i}nez and Dante Travisany and Bruno Defilippi and Mauricio Gonz\'{a}lez-Ag\"{u}ero and Sam Cherian and Lida Fuentes}, url = {http://www.sciencedirect.com/science/article/pii/S0304423818306952}, doi = {https://doi.org/10.1016/j.scienta.2018.09.077}, issn = {0304-4238}, year = {2019}, date = {2019-01-01}, journal = {Scientia Horticulturae}, volume = {246}, pages = {168 -- 175}, abstract = {The conjugation of indole-3-acetic acid (IAA) to amino acids by indole-3-acetic acid (IAA)-amido synthetases (GH3) is an important part of auxin level regulation. However, the auxin conjugation during development of soft fruits such as raspberry is poorly understood. In this study, indole-3-acetic acid (IAA)-amido synthetases in raspberry, designated as RiGH3 (RiGH3.1, RiGH3.5 transcripts) were evaluated during fruit development of raspberry cultivar Rubus idaeus Heritage, and under IAA treatment. The results showed that before to the onset of ripening the fruit size, weight and the expression of IAA-amido synthetase RiGH3.1 transcript levels increased. Then when the fruits attain full development, fruit firmness and titratable acidity decreased, in the contrast to ethylene production and total soluble solids content increasing. However, the RiGH3.5 transcript was found to be expressed primarily in flowers. When compared to untreated control fruit, fruit treated with 1 mM of IAA at white stage, showed an increase of RiGH3.1 transcript during in-vitro assay (10 °C by 18 h). However, no significant change in the levels of RiGH3.5 was observed during IAA treatment. Multiple alignments of the full-length predicted RiGH3.1 protein sequences revealed a high sequence homology with proteins deduced sequences described for other fruit of Rosaceae species. The RiGH3.1 deduced sequence showed the presence of binding motives for IAA and aspartic acid, and indicate that the isolated sequence have the typical motives of GH3.1 protein family. These findings give new insights into the possible role of RiGH3.1 transcripts, and the IAA conjugation (in maintaining the low concentration of free IAA) during raspberry fruit ripening.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The conjugation of indole-3-acetic acid (IAA) to amino acids by indole-3-acetic acid (IAA)-amido synthetases (GH3) is an important part of auxin level regulation. However, the auxin conjugation during development of soft fruits such as raspberry is poorly understood. In this study, indole-3-acetic acid (IAA)-amido synthetases in raspberry, designated as RiGH3 (RiGH3.1, RiGH3.5 transcripts) were evaluated during fruit development of raspberry cultivar Rubus idaeus Heritage, and under IAA treatment. The results showed that before to the onset of ripening the fruit size, weight and the expression of IAA-amido synthetase RiGH3.1 transcript levels increased. Then when the fruits attain full development, fruit firmness and titratable acidity decreased, in the contrast to ethylene production and total soluble solids content increasing. However, the RiGH3.5 transcript was found to be expressed primarily in flowers. When compared to untreated control fruit, fruit treated with 1 mM of IAA at white stage, showed an increase of RiGH3.1 transcript during in-vitro assay (10 °C by 18 h). However, no significant change in the levels of RiGH3.5 was observed during IAA treatment. Multiple alignments of the full-length predicted RiGH3.1 protein sequences revealed a high sequence homology with proteins deduced sequences described for other fruit of Rosaceae species. The RiGH3.1 deduced sequence showed the presence of binding motives for IAA and aspartic acid, and indicate that the isolated sequence have the typical motives of GH3.1 protein family. These findings give new insights into the possible role of RiGH3.1 transcripts, and the IAA conjugation (in maintaining the low concentration of free IAA) during raspberry fruit ripening. |
Díaz, VB; Schleicher, DRG; Bovino, S; Riaz, R; Vanaverbeke, S; Olave, C Impact of radiation backgrounds on the formation of massive black holes Technical Report 2019. @techreport{diaz_impact_2019, title = {Impact of radiation backgrounds on the formation of massive black holes}, author = {VB D\'{i}az and DRG Schleicher and S Bovino and R Riaz and S Vanaverbeke and C Olave}, url = {http://www.swmath.org/software/1046}, year = {2019}, date = {2019-01-01}, abstract = {Resumen / La existencia de agujeros negros supermasivos de mil millones de masas solares a muy alto corri-miento al rojo nos ha motivado a estudiar como estos objetos tan masivos se forman durante los primeros miles de millones de a\~{n}os despu\'{e}s del Big Bang. El modelo mas prometedor que se ha propuesto es el colapso directo de nubes de gas protogal\'{a}cticas. Este escenario requiere altas tasas de acreci\'{o}n para crear r\'{a}pidamente objetos masi-vos y la inhibici\'{o}n del enfriamiento que causa H2, el cu\'{a}l es importante en el proceso de fragmentaci\'{o}n. Estudios recientes mostraron que, si usamos un fondo radiativo fuerte, el hidr\'{o}geno molecular se destruye, favoreciendo las altas tasas de acreci\'{o}n y por lo tanto formando objetos de muy alta masa. En este trabajo estudiamos el impacto de campos de radiaci\'{o}n UV en una nube de gas primordial usando el c\'{o}digo GRADSPH-KROME para investigar el proceso de fragmentaci\'{o}n en escalas de unidades astron\'{o}micas y por lo tanto la formaci\'{o}n de los primeros agujeros negros supermasivos. Encontramos que para suprimir la formaci\'{o}n de H2 es necesario un valor de J21 muy alto, por lo que los agujeros negros de colapso directo no podr\'{i}an explicar la formaci\'{o}n de los primeros agujeros negros supermasivos. Abstract / The presence of supermassive black holes (SMBHs) of a few billion solar masses at very high redshift has motivated us to study how these massive objects formed during the first billion years after the Big Bang. The most promising model that has been proposed to explain this is the direct collapse of protogalactic gas clouds. In this scenario, very high accretion rates are needed to form massive objects early on and the suppression of H2 cooling is important in regulating the fragmentation. Recent studies have shown that if we use a strong radiation background, the hydrogen molecules are destroyed, favoring the high accretion rates and therefore producing objects of very high mass. In this work we study the impact of UV radiation fields in a primordial gas cloud using the recently coupled code GRADSPH-KROME for the modeling of gravitational collapse including primordial chemistry to explore the fragmentation in AU scales and hence the formation of first SMBHs. We found that to suppress the formation of H2 a very high value of J21 is required, because of that we conclude that the direct collapse black holes (DCBHs) are very unlikely to be an explanation for the formation of the first SMBHs.}, keywords = {}, pubstate = {published}, tppubtype = {techreport} } Resumen / La existencia de agujeros negros supermasivos de mil millones de masas solares a muy alto corri-miento al rojo nos ha motivado a estudiar como estos objetos tan masivos se forman durante los primeros miles de millones de años después del Big Bang. El modelo mas prometedor que se ha propuesto es el colapso directo de nubes de gas protogalácticas. Este escenario requiere altas tasas de acreción para crear rápidamente objetos masi-vos y la inhibición del enfriamiento que causa H2, el cuál es importante en el proceso de fragmentación. Estudios recientes mostraron que, si usamos un fondo radiativo fuerte, el hidrógeno molecular se destruye, favoreciendo las altas tasas de acreción y por lo tanto formando objetos de muy alta masa. En este trabajo estudiamos el impacto de campos de radiación UV en una nube de gas primordial usando el código GRADSPH-KROME para investigar el proceso de fragmentación en escalas de unidades astronómicas y por lo tanto la formación de los primeros agujeros negros supermasivos. Encontramos que para suprimir la formación de H2 es necesario un valor de J21 muy alto, por lo que los agujeros negros de colapso directo no podrían explicar la formación de los primeros agujeros negros supermasivos. Abstract / The presence of supermassive black holes (SMBHs) of a few billion solar masses at very high redshift has motivated us to study how these massive objects formed during the first billion years after the Big Bang. The most promising model that has been proposed to explain this is the direct collapse of protogalactic gas clouds. In this scenario, very high accretion rates are needed to form massive objects early on and the suppression of H2 cooling is important in regulating the fragmentation. Recent studies have shown that if we use a strong radiation background, the hydrogen molecules are destroyed, favoring the high accretion rates and therefore producing objects of very high mass. In this work we study the impact of UV radiation fields in a primordial gas cloud using the recently coupled code GRADSPH-KROME for the modeling of gravitational collapse including primordial chemistry to explore the fragmentation in AU scales and hence the formation of first SMBHs. We found that to suppress the formation of H2 a very high value of J21 is required, because of that we conclude that the direct collapse black holes (DCBHs) are very unlikely to be an explanation for the formation of the first SMBHs. |
Davis, Sergio; Loyola, Claudia; Peralta, Joaquín Bayesian statistical modeling of microcanonical melting times at the superheated regime Journal Article Physica A: Statistical Mechanics and its Applications, 515 , pp. 546 – 557, 2019, ISSN: 0378-4371. @article{davis_bayesian_2019, title = {Bayesian statistical modeling of microcanonical melting times at the superheated regime}, author = {Sergio Davis and Claudia Loyola and Joaqu\'{i}n Peralta}, url = {http://www.sciencedirect.com/science/article/pii/S0378437118313037}, doi = {https://doi.org/10.1016/j.physa.2018.09.174}, issn = {0378-4371}, year = {2019}, date = {2019-01-01}, journal = {Physica A: Statistical Mechanics and its Applications}, volume = {515}, pages = {546 -- 557}, abstract = {Homogeneous melting of superheated crystals at constant energy is a dynamical process, believed to be triggered by the accumulation of thermal vacancies and their self-diffusion. From microcanonical simulations we know that if an ideal crystal is prepared at a given kinetic energy, it takes a random time tw until the melting mechanism is actually triggered. In this work we have studied in detail the statistics of tw for melting at different energies by performing a large number of Z-method simulations and applying state-of-the-art methods of Bayesian statistical inference. By focusing on a small system size and short-time tail of the distribution function, we show that tw is actually gamma-distributed rather than exponential (as asserted in a previous work), with decreasing probability near tw∼0. We also explicitly incorporate in our model the unavoidable truncation of the distribution function due to the limited total time span of a Z-method simulation. The probabilistic model presented in this work can provide some insight into the dynamical nature of the homogeneous melting process, as well as giving a well-defined practical procedure to incorporate melting times from simulation into the Z-method in order to correct the effect of short simulation times.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Homogeneous melting of superheated crystals at constant energy is a dynamical process, believed to be triggered by the accumulation of thermal vacancies and their self-diffusion. From microcanonical simulations we know that if an ideal crystal is prepared at a given kinetic energy, it takes a random time tw until the melting mechanism is actually triggered. In this work we have studied in detail the statistics of tw for melting at different energies by performing a large number of Z-method simulations and applying state-of-the-art methods of Bayesian statistical inference. By focusing on a small system size and short-time tail of the distribution function, we show that tw is actually gamma-distributed rather than exponential (as asserted in a previous work), with decreasing probability near tw∼0. We also explicitly incorporate in our model the unavoidable truncation of the distribution function due to the limited total time span of a Z-method simulation. The probabilistic model presented in this work can provide some insight into the dynamical nature of the homogeneous melting process, as well as giving a well-defined practical procedure to incorporate melting times from simulation into the Z-method in order to correct the effect of short simulation times. |
Banegas-Luna, Antonio Jesús; Imbernón, Baldomero; Castro, Antonio Llanes; Pérez-Garrido, Alfonso; Cerón-Carrasco, José Pedro; Gesing, Sandra; Merelli, Ivan; D’Agostino, Daniele; Pérez-Sánchez, Horacio Advances in distributed computing with modern drug discovery Journal Article Expert Opinion on Drug Discovery, 14 (1), pp. 9–22, 2019. @article{banegas-luna_advances_2019, title = {Advances in distributed computing with modern drug discovery}, author = {Antonio Jes\'{u}s Banegas-Luna and Baldomero Imbern\'{o}n and Antonio Llanes Castro and Alfonso P\'{e}rez-Garrido and Jos\'{e} Pedro Cer\'{o}n-Carrasco and Sandra Gesing and Ivan Merelli and Daniele D’Agostino and Horacio P\'{e}rez-S\'{a}nchez}, url = {https://doi.org/10.1080/17460441.2019.1552936}, doi = {10.1080/17460441.2019.1552936}, year = {2019}, date = {2019-01-01}, journal = {Expert Opinion on Drug Discovery}, volume = {14}, number = {1}, pages = {9--22}, abstract = {ABSTRACTIntroduction: Computational chemistry dramatically accelerates the drug discovery process and high-performance computing (HPC) can be used to speed up the most expensive calculations. Supporting a local HPC infrastructure is both costly and time-consuming, and, therefore, many research groups are moving from in-house solutions to remote-distributed computing platforms.Areas covered: The authors focus on the use of distributed technologies, solutions, and infrastructures to gain access to HPC capabilities, software tools, and datasets to run the complex simulations required in computational drug discovery (CDD).Expert opinion: The use of computational tools can decrease the time to market of new drugs. HPC has a crucial role in handling the complex algorithms and large volumes of data required to achieve specificity and avoid undesirable side-effects. Distributed computing environments have clear advantages over in-house solutions in terms of cost and sustainability. The use of infrastructures relying on virtualization reduces set-up costs. Distributed computing resources can be difficult to access, although web-based solutions are becoming increasingly available. There is a trade-off between cost-effectiveness and accessibility in using on-demand computing resources rather than free/academic resources. Graphics processing unit computing, with its outstanding parallel computing power, is becoming increasingly important.}, keywords = {}, pubstate = {published}, tppubtype = {article} } ABSTRACTIntroduction: Computational chemistry dramatically accelerates the drug discovery process and high-performance computing (HPC) can be used to speed up the most expensive calculations. Supporting a local HPC infrastructure is both costly and time-consuming, and, therefore, many research groups are moving from in-house solutions to remote-distributed computing platforms.Areas covered: The authors focus on the use of distributed technologies, solutions, and infrastructures to gain access to HPC capabilities, software tools, and datasets to run the complex simulations required in computational drug discovery (CDD).Expert opinion: The use of computational tools can decrease the time to market of new drugs. HPC has a crucial role in handling the complex algorithms and large volumes of data required to achieve specificity and avoid undesirable side-effects. Distributed computing environments have clear advantages over in-house solutions in terms of cost and sustainability. The use of infrastructures relying on virtualization reduces set-up costs. Distributed computing resources can be difficult to access, although web-based solutions are becoming increasingly available. There is a trade-off between cost-effectiveness and accessibility in using on-demand computing resources rather than free/academic resources. Graphics processing unit computing, with its outstanding parallel computing power, is becoming increasingly important. |
Menéndez-Proupin, E; Casanova-Páez, M; Montero-Alejo, A L; Flores, M A; Orellana, W Symmetry and thermodynamics of tellurium vacancies in cadmium telluride Journal Article Physica B: Condensed Matter, 2019, ISSN: 0921-4526. @article{menendez-proupin_symmetry_2019, title = {Symmetry and thermodynamics of tellurium vacancies in cadmium telluride}, author = {E Men\'{e}ndez-Proupin and M Casanova-P\'{a}ez and A L Montero-Alejo and M A Flores and W Orellana}, url = {http://www.sciencedirect.com/science/article/pii/S0921452619300134}, doi = {https://doi.org/10.1016/j.physb.2019.01.013}, issn = {0921-4526}, year = {2019}, date = {2019-01-01}, journal = {Physica B: Condensed Matter}, abstract = {The equilibrium geometries and thermodynamic properties of anion vacancies in cadmium telluride, as predicted by density functional theory, are revisited using semilocal and hybrid density functionals. We find that stable configurations in different charge states can only be found after a systematic search considering several starting geometries. The stable charge states, 0 and 2+, display closed-shell electronic configurations, without deep bandgap levels. The 2 + charge state has a Td symmetry with an outward relaxation, while the neutral state is a mixture of configurations with C2v and C3v symmetries, both with the same energy and a negligible energy barrier. Therefore, the neutral charge state presents an effective Td symmetry. Configurations with different symmetries, e.g., D2d, can exist as metastable states. We show that certain configurations may seem falsely stable due to several facts: the bandgap error of generalized gradient approximation, the k-point sampling used in small supercells, or the use of a restricted set of starting geometries. We believe that the HSE06 hybrid functional allows to obtain accurate formation energies and geometries. We analyze the effect of the spin-orbit coupling and GW quasiparticle corrections to the HSE06 results, and find no qualitative differences. The spin-orbit coupling and GW corrections to the HSE06 energies partially cancel each other. Finally, we investigate the divacancy VCdVTe. The obtained formation energies suggest that isolated tellurium vacancies in neutral charge state can be found only in Te-poor growth conditions, coexisting with divacancies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The equilibrium geometries and thermodynamic properties of anion vacancies in cadmium telluride, as predicted by density functional theory, are revisited using semilocal and hybrid density functionals. We find that stable configurations in different charge states can only be found after a systematic search considering several starting geometries. The stable charge states, 0 and 2+, display closed-shell electronic configurations, without deep bandgap levels. The 2 + charge state has a Td symmetry with an outward relaxation, while the neutral state is a mixture of configurations with C2v and C3v symmetries, both with the same energy and a negligible energy barrier. Therefore, the neutral charge state presents an effective Td symmetry. Configurations with different symmetries, e.g., D2d, can exist as metastable states. We show that certain configurations may seem falsely stable due to several facts: the bandgap error of generalized gradient approximation, the k-point sampling used in small supercells, or the use of a restricted set of starting geometries. We believe that the HSE06 hybrid functional allows to obtain accurate formation energies and geometries. We analyze the effect of the spin-orbit coupling and GW quasiparticle corrections to the HSE06 results, and find no qualitative differences. The spin-orbit coupling and GW corrections to the HSE06 energies partially cancel each other. Finally, we investigate the divacancy VCdVTe. The obtained formation energies suggest that isolated tellurium vacancies in neutral charge state can be found only in Te-poor growth conditions, coexisting with divacancies. |
Martínez-Cifuentes, Maximiliano; Monroy-Cárdenas, Matías; Millas-Vargas, Juan Pablo; Weiss-López, Boris E; Araya-Maturana, Ramiro Assessing Parameter Suitability for the Strength Evaluation of Intramolecular Resonance Assisted Hydrogen Bonding in o-Carbonyl Hydroquinones Journal Article Molecules, 24 (2), 2019, ISSN: 1420-3049. @article{martinez-cifuentes_assessing_2019, title = {Assessing Parameter Suitability for the Strength Evaluation of Intramolecular Resonance Assisted Hydrogen Bonding in o-Carbonyl Hydroquinones}, author = {Maximiliano Mart\'{i}nez-Cifuentes and Mat\'{i}as Monroy-C\'{a}rdenas and Juan Pablo Millas-Vargas and Boris E Weiss-L\'{o}pez and Ramiro Araya-Maturana}, url = {http://www.mdpi.com/1420-3049/24/2/280}, doi = {10.3390/molecules24020280}, issn = {1420-3049}, year = {2019}, date = {2019-01-01}, journal = {Molecules}, volume = {24}, number = {2}, abstract = {Intramolecular hydrogen bond (IMHB) interactions have attracted considerable attention due to their central role in molecular structure, chemical reactivity, and interactions of biologically active molecules. Precise correlations of the strength of IMHB’s with experimental parameters are a key goal in order to model compounds for drug discovery. In this work, we carry out an experimental (NMR) and theoretical (DFT) study of the IMHB in a series of structurally similar o-carbonyl hydroquinones. Geometrical parameters, as well as Natural Bond Orbital (NBO) and Quantum Theory of Atoms in Molecules (QTAIM) parameters for IMHB were compared with experimental NMR data. Three DFT functionals were employed to calculated theoretical parameters: B3LYP, M06-2X, and ωB97XD. O…H distance is the most suitable geometrical parameter to distinguish among similar IMHBs. Second order stabilization energies ΔEij(2) from NBO analysis and hydrogen bond energy (EHB) obtained from QTAIM analysis also properly distinguishes the order in strength of the studied IMHB. ΔEij(2) from NBO give values for the IMHB below 30 kcal/mol, while EHB from QTAIM analysis give values above 30 kcal/mol. In all cases, the calculated parameters using ωB97XD give the best correlations with experimental 1H-NMR chemical shifts for the IMHB, with R2 values around 0.89. Although the results show that these parameters correctly reflect the strength of the IMHB, when the weakest one is removed from the analysis, arguing experimental considerations, correlations improve significantly to values around 0.95 for R2.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Intramolecular hydrogen bond (IMHB) interactions have attracted considerable attention due to their central role in molecular structure, chemical reactivity, and interactions of biologically active molecules. Precise correlations of the strength of IMHB’s with experimental parameters are a key goal in order to model compounds for drug discovery. In this work, we carry out an experimental (NMR) and theoretical (DFT) study of the IMHB in a series of structurally similar o-carbonyl hydroquinones. Geometrical parameters, as well as Natural Bond Orbital (NBO) and Quantum Theory of Atoms in Molecules (QTAIM) parameters for IMHB were compared with experimental NMR data. Three DFT functionals were employed to calculated theoretical parameters: B3LYP, M06-2X, and ωB97XD. O…H distance is the most suitable geometrical parameter to distinguish among similar IMHBs. Second order stabilization energies ΔEij(2) from NBO analysis and hydrogen bond energy (EHB) obtained from QTAIM analysis also properly distinguishes the order in strength of the studied IMHB. ΔEij(2) from NBO give values for the IMHB below 30 kcal/mol, while EHB from QTAIM analysis give values above 30 kcal/mol. In all cases, the calculated parameters using ωB97XD give the best correlations with experimental 1H-NMR chemical shifts for the IMHB, with R2 values around 0.89. Although the results show that these parameters correctly reflect the strength of the IMHB, when the weakest one is removed from the analysis, arguing experimental considerations, correlations improve significantly to values around 0.95 for R2. |
Urzua-Leiva, Rodrigo; Pino-Rios, Ricardo; Cardenas-Jiron, Gloria Phys. Chem. Chem. Phys., pp. –, 2019. @article{urzua-leiva_influence_2019, title = {The Influence of Antenna and Anchoring Moieties on the Improvement of Photoelectronic Properties in Zn(II)-Porphyrin-TiO2 as Potential Dye-Sensitized Solar Cells}, author = {Rodrigo Urzua-Leiva and Ricardo Pino-Rios and Gloria Cardenas-Jiron}, url = {http://dx.doi.org/10.1039/C8CP06988C}, doi = {10.1039/C8CP06988C}, year = {2019}, date = {2019-01-01}, journal = {Phys. Chem. Chem. Phys.}, pages = {--}, abstract = {A systematic study for the rational design of porphyrins (P4 spider-shaped derivatives) with potential application in dye-sensitized solar cells is presented. Using density functional theory (DFT) (B3LYP/6-31G*) and time-dependent DFT (M06/6-31G*) we show that the UV-vis absorption properties of a spider-shaped Zn(II) porphyrin, previously synthesized by Stangel et al., may be greatly improved by applying some push-pull strategies in meso positions. We found that the selected triphenylamine push group induces a remarkable improvement in the absorption bands of P4 spider-shaped derivatives. The pull effect reached through the π-electron-rich phenyl group and the benzodithiazole (BTD) group, allowed the Q bands to be red-shifted up to 689 nm, much longer than the 593 nm reported experimentally for the original spider-shaped porphyrin. The adsorption results of the P4 spider-shaped derivatives onto a TiO2-anatase surface model [Ti16O34H4] through the carboxylic acid group showed that the adsorptions energies were favourable and very similar in all cases. Natural bond orbitals (NBO) indicated a two-center bond (BD) O(carboxyl)-Ti(TiO2) for the porphyrin with the highest adsorption energy (8.27 kcal/mol), and donor acceptor interactions from LP O(carboxyl) to Ti(TiO2) for the other porphyrins. The natural transition orbitals (NTO) for P4-derivatives-TiO2 confirm the nature of the excited states associated with Q and Soret bands. Finally, the frontier molecular orbitals revealed charge-separated states between those occupied and unoccupied, indicating a favourable charge-transfer process between the dyes and the surface conduction bands. In conclusion, this work showed a systematic study based in the push-pull strategy that improves the performance of porphyrins with the purpose to be used in dye-sensitized solar cells.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A systematic study for the rational design of porphyrins (P4 spider-shaped derivatives) with potential application in dye-sensitized solar cells is presented. Using density functional theory (DFT) (B3LYP/6-31G*) and time-dependent DFT (M06/6-31G*) we show that the UV-vis absorption properties of a spider-shaped Zn(II) porphyrin, previously synthesized by Stangel et al., may be greatly improved by applying some push-pull strategies in meso positions. We found that the selected triphenylamine push group induces a remarkable improvement in the absorption bands of P4 spider-shaped derivatives. The pull effect reached through the π-electron-rich phenyl group and the benzodithiazole (BTD) group, allowed the Q bands to be red-shifted up to 689 nm, much longer than the 593 nm reported experimentally for the original spider-shaped porphyrin. The adsorption results of the P4 spider-shaped derivatives onto a TiO2-anatase surface model [Ti16O34H4] through the carboxylic acid group showed that the adsorptions energies were favourable and very similar in all cases. Natural bond orbitals (NBO) indicated a two-center bond (BD) O(carboxyl)-Ti(TiO2) for the porphyrin with the highest adsorption energy (8.27 kcal/mol), and donor acceptor interactions from LP O(carboxyl) to Ti(TiO2) for the other porphyrins. The natural transition orbitals (NTO) for P4-derivatives-TiO2 confirm the nature of the excited states associated with Q and Soret bands. Finally, the frontier molecular orbitals revealed charge-separated states between those occupied and unoccupied, indicating a favourable charge-transfer process between the dyes and the surface conduction bands. In conclusion, this work showed a systematic study based in the push-pull strategy that improves the performance of porphyrins with the purpose to be used in dye-sensitized solar cells. |
Valenzuela, Gerson E Computer Simulation of the Effect of Wetting Conditions on the Solvation Force and Pull-Off Force of Water Confined between Two Flat Substrates Journal Article JOURNAL OF PHYSICAL CHEMISTRY C, 123 (2), pp. 1252–1259, 2019, ISSN: 1932-7447. @article{valenzuela_computer_2019, title = {Computer Simulation of the Effect of Wetting Conditions on the Solvation Force and Pull-Off Force of Water Confined between Two Flat Substrates}, author = {Gerson E Valenzuela}, doi = {10.1021/acs.jpcc.8b09907}, issn = {1932-7447}, year = {2019}, date = {2019-01-01}, journal = {JOURNAL OF PHYSICAL CHEMISTRY C}, volume = {123}, number = {2}, pages = {1252--1259}, abstract = {Modeling experimental results of pull-off versus relative humidity obtained by atomic force microscopy (AFM) has suggested that the classic interaction force models (van der Waals and capillarity) do not capture the water behavior confined between two surfaces at a distance D approximate to 1 nm. In this paper, pull-off generated by bridges of water confined between two flat substrates is studied using molecular dynamics simulations, varying the wetting conditions and the number of water molecules of the bridge. The method used imitates the approach and retraction curves in AFM. The confined water exhibits an oscillatory solvation force for D textless 1.3 nm for both hydrophilic and hydrophobic surfaces. For hydrophilic surfaces, the pull-off corresponds precisely to the maximum of attractive force produced at D approximate to 0.7 nm, where the bridge is composed of two water layers. These results are applicable to the tip-sample nanocontact of experimental systems for substrates at a contact angle textgreater40 degrees.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Modeling experimental results of pull-off versus relative humidity obtained by atomic force microscopy (AFM) has suggested that the classic interaction force models (van der Waals and capillarity) do not capture the water behavior confined between two surfaces at a distance D approximate to 1 nm. In this paper, pull-off generated by bridges of water confined between two flat substrates is studied using molecular dynamics simulations, varying the wetting conditions and the number of water molecules of the bridge. The method used imitates the approach and retraction curves in AFM. The confined water exhibits an oscillatory solvation force for D textless 1.3 nm for both hydrophilic and hydrophobic surfaces. For hydrophilic surfaces, the pull-off corresponds precisely to the maximum of attractive force produced at D approximate to 0.7 nm, where the bridge is composed of two water layers. These results are applicable to the tip-sample nanocontact of experimental systems for substrates at a contact angle textgreater40 degrees. |
Poch, Andrea; Villanelo, Felipe; Henriquez, Soledad; Kohen, Paulina; Muñoz, Alex; Strauss, Jerome F; Devoto, Luigi Molecular modelling predicts that 2-methoxyestradiol disrupts HIF function by binding to the PAS-B domain Journal Article Steroids, 2019, ISSN: 0039-128X. @article{poch_molecular_2019, title = {Molecular modelling predicts that 2-methoxyestradiol disrupts HIF function by binding to the PAS-B domain}, author = {Andrea Poch and Felipe Villanelo and Soledad Henriquez and Paulina Kohen and Alex Mu\~{n}oz and Jerome F Strauss and Luigi Devoto}, url = {http://www.sciencedirect.com/science/article/pii/S0039128X19300212}, doi = {https://doi.org/10.1016/j.steroids.2019.02.004}, issn = {0039-128X}, year = {2019}, date = {2019-01-01}, journal = {Steroids}, abstract = {An estradiol metabolite, 2-methoxyestradiol (2ME), has emerged as an important regulator of ovarian physiology. 2ME is recognized as a potent anti-angiogenic agent in clinical trials and laboratory studies. However, little is known about its molecular actions and its endogenous targets. 2ME is produced by human ovarian cells during the normal menstrual cycle, being higher during regression of the corpus luteum, and is postulated to be involved in the anti-angiogenic process that plays out during luteolysis. We utilized cell biology techniques to understand the molecular mechanism of 2ME anti-angiogenic effects on human granulosa luteal cells. The principal effect of 2ME was to alter Hypoxia Inducible Factor 1A (HIF1A) sub-cellular localization. Molecular modelling and multiple bioinformatics tools indicated that 2ME impairs Hypoxia Inducible Factor complex (HIF) nuclear translocation by binding to a buried pocket in the HIF1A Per Arnt Sim (PAS)-B domain. Binding of 2ME to HIF1A protein is predicted to perturb HIF1A-Hypoxia Inducible Factor B (HIFB) interaction, a key step in HIF nuclear translocation, preventing the transcriptional actions of HIF, including Vascular Endotelial Growth Factor (VEGF) gene activation. To our knowledge, 2ME is the first putative HIF endogenous ligand characterized with anti-angiogenic activity. This postulate has important implications for reproduction, because angiogenic processes are critical for ovarian follicular development, ovulation and corpus luteum regression. The present research could contribute to the development of novel pharmacological approaches for controlling HIF activity in human reproductive diseases.}, keywords = {}, pubstate = {published}, tppubtype = {article} } An estradiol metabolite, 2-methoxyestradiol (2ME), has emerged as an important regulator of ovarian physiology. 2ME is recognized as a potent anti-angiogenic agent in clinical trials and laboratory studies. However, little is known about its molecular actions and its endogenous targets. 2ME is produced by human ovarian cells during the normal menstrual cycle, being higher during regression of the corpus luteum, and is postulated to be involved in the anti-angiogenic process that plays out during luteolysis. We utilized cell biology techniques to understand the molecular mechanism of 2ME anti-angiogenic effects on human granulosa luteal cells. The principal effect of 2ME was to alter Hypoxia Inducible Factor 1A (HIF1A) sub-cellular localization. Molecular modelling and multiple bioinformatics tools indicated that 2ME impairs Hypoxia Inducible Factor complex (HIF) nuclear translocation by binding to a buried pocket in the HIF1A Per Arnt Sim (PAS)-B domain. Binding of 2ME to HIF1A protein is predicted to perturb HIF1A-Hypoxia Inducible Factor B (HIFB) interaction, a key step in HIF nuclear translocation, preventing the transcriptional actions of HIF, including Vascular Endotelial Growth Factor (VEGF) gene activation. To our knowledge, 2ME is the first putative HIF endogenous ligand characterized with anti-angiogenic activity. This postulate has important implications for reproduction, because angiogenic processes are critical for ovarian follicular development, ovulation and corpus luteum regression. The present research could contribute to the development of novel pharmacological approaches for controlling HIF activity in human reproductive diseases. |
2018 |
Shene, Carolina; Garcés, Marcelo; Vergara, Daniela; ñ, Jhonatan Pe; Claverol, Stéphane; Rubilar, Mónica; Leyton, Allison Production of Lipids and Proteome Variation in a Chilean Thraustochytrium striatum Strain Cultured under Different Growth Conditions Journal Article Marine Biotechnology, 2018, ISSN: 1436-2236. @article{Shene2018, title = {Production of Lipids and Proteome Variation in a Chilean Thraustochytrium striatum Strain Cultured under Different Growth Conditions}, author = {Carolina Shene and Marcelo Garc\'{e}s and Daniela Vergara and Jhonatan Pe{\~{n}}a and St\'{e}phane Claverol and M\'{o}nica Rubilar and Allison Leyton}, url = {https://doi.org/10.1007/s10126-018-9863-z}, doi = {10.1007/s10126-018-9863-z}, issn = {1436-2236}, year = {2018}, date = {2018-11-19}, journal = {Marine Biotechnology}, abstract = {Total lipids and docosahexaenoic acid (DHA) production by a Chilean isolated thraustochytrid were evaluated under different growth conditions in shake flasks. The analyzed strain was identified as Thraustochytrium striatum according to an 18S rRNA gene sequence analysis. The strain (T. striatum AL16) showed negligible growth in media prepared with artificial seawater at concentrations lower than 50% v/v and pH lower than 5. Maltose and starch were better carbon sources for growth than glucose. DHA content of the biomass grown with maltose (60 g L−1) was doubled by increasing the agitation rate from 150 to 250 rpm. The DHA (0.8--6%) and eicosapentaenoic acid (0.2--21%) content in the total lipids varied depending on culture conditions and culture age. Lipid and DHA concentration increased (up to 5 g L−1 and 66 mg L−1, respectively) by regularly feeding the culture with a concentrated starch solution. Carotenoid accumulation was detected in cells grown with maltose or starch. Contrasting conditions of starch and glucose cultures were selected for comparative proteomics. Total protein extracts were separated by two-dimensional gel electrophoresis; 25 spots were identified using ESI-MS/MS. A protein database (143,006 entries) for proteomic interrogation was generated using de novo assembling of Thraustochytrium sp. LLF1b -- MMETSP0199_2 transcriptome; 18 proteins differentially expressed were identified. Three ATP synthases were differentially accumulated in cultures with glucose, whereas malate dehydrogenase was more abundant in cells cultured with starch.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Total lipids and docosahexaenoic acid (DHA) production by a Chilean isolated thraustochytrid were evaluated under different growth conditions in shake flasks. The analyzed strain was identified as Thraustochytrium striatum according to an 18S rRNA gene sequence analysis. The strain (T. striatum AL16) showed negligible growth in media prepared with artificial seawater at concentrations lower than 50% v/v and pH lower than 5. Maltose and starch were better carbon sources for growth than glucose. DHA content of the biomass grown with maltose (60 g L−1) was doubled by increasing the agitation rate from 150 to 250 rpm. The DHA (0.8--6%) and eicosapentaenoic acid (0.2--21%) content in the total lipids varied depending on culture conditions and culture age. Lipid and DHA concentration increased (up to 5 g L−1 and 66 mg L−1, respectively) by regularly feeding the culture with a concentrated starch solution. Carotenoid accumulation was detected in cells grown with maltose or starch. Contrasting conditions of starch and glucose cultures were selected for comparative proteomics. Total protein extracts were separated by two-dimensional gel electrophoresis; 25 spots were identified using ESI-MS/MS. A protein database (143,006 entries) for proteomic interrogation was generated using de novo assembling of Thraustochytrium sp. LLF1b -- MMETSP0199_2 transcriptome; 18 proteins differentially expressed were identified. Three ATP synthases were differentially accumulated in cultures with glucose, whereas malate dehydrogenase was more abundant in cells cultured with starch. |
José, ; Raúl, ; Suárez, Francisco Exploring the interactions between hydrodynamics and fouling in membrane distillation systems – A multiscale approach using CFD Journal Article Desalination, 444 , pp. 63–74, 2018. @article{Amigo2018, title = {Exploring the interactions between hydrodynamics and fouling in membrane distillation systems \textendash A multiscale approach using CFD}, author = {Jos\'{e} and Ra\'{u}l and Francisco Su\'{a}rez}, url = {https://doi.org/10.1016/j.desal.2018.07.009}, doi = {10.1016/j.desal.2018.07.009}, year = {2018}, date = {2018-10-01}, journal = {Desalination}, volume = {444}, pages = {63--74}, publisher = {Elsevier BV}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
ú, Fabián Díaz-N; Quezada, Franco; á, Óscar C V The knapsack problem with scheduled items Journal Article Electronic Notes in Discrete Mathematics, 69 , pp. 293–300, 2018. @article{DazNez2018, title = {The knapsack problem with scheduled items}, author = {Fabi\'{a}n D\'{i}az-N{\'{u}} \~{n} and Franco Quezada and \'{O}scar C V \'{a}}, url = {https://doi.org/10.1016/j.endm.2018.07.038}, doi = {10.1016/j.endm.2018.07.038}, year = {2018}, date = {2018-08-01}, journal = {Electronic Notes in Discrete Mathematics}, volume = {69}, pages = {293--300}, publisher = {Elsevier BV}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
é, Diego Cort; Ortega, Daniela E Effects on the aromatic character of DNA/RNA nucleobases due to its adsorption onto graphene Journal Article International Journal of Quantum Chemistry, pp. e25699, 2018. @article{CortsArriagada2018, title = {Effects on the aromatic character of DNA/RNA nucleobases due to its adsorption onto graphene}, author = {Diego Cort \'{e} and Daniela E Ortega}, url = {https://doi.org/10.1002/qua.25699}, doi = {10.1002/qua.25699}, year = {2018}, date = {2018-08-01}, journal = {International Journal of Quantum Chemistry}, pages = {e25699}, publisher = {Wiley}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Vargas, Brenda; ú, Ra; á, Joelis Rodríguez-Hern; Gembicky, Milan; Xie, Haomiao; é, José Jim; Liu, Yi-Sheng; é, Eduardo Men; Dunbar, Kim R; Lopez, Nazario; Olalde-Velasco, Paul; Solis-Ibarra, Diego Optical, Electronic and Magnetic Engineering of 〈111〉 Layered Halide Perovskites Journal Article Chemistry of Materials, 2018. @article{Vargas2018, title = {Optical, Electronic and Magnetic Engineering of 〈111〉 Layered Halide Perovskites}, author = {Brenda Vargas and Ra \'{u} and Joelis Rodr\'{i}guez-Hern \'{a} and Milan Gembicky and Haomiao Xie and Jos\'{e} Jim \'{e} and Yi-Sheng Liu and Eduardo Men \'{e} and Kim R Dunbar and Nazario Lopez and Paul Olalde-Velasco and Diego Solis-Ibarra}, url = {https://doi.org/10.1021/acs.chemmater.8b02099}, doi = {10.1021/acs.chemmater.8b02099}, year = {2018}, date = {2018-07-01}, journal = {Chemistry of Materials}, publisher = {American Chemical Society (ACS)}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Riaz, R; Vanaverbeke, S; Schleicher, D R G Episodic accretion in binary protostars emerging from self-gravitating solar mass cores Journal Article Astronomy & Astrophysics, 614 , pp. A53, 2018. @article{Riaz2018, title = {Episodic accretion in binary protostars emerging from self-gravitating solar mass cores}, author = {R Riaz and S Vanaverbeke and D R G Schleicher}, url = {https://doi.org/10.1051/0004-6361/201732076}, doi = {10.1051/0004-6361/201732076}, year = {2018}, date = {2018-06-01}, journal = {Astronomy & Astrophysics}, volume = {614}, pages = {A53}, publisher = {EDP Sciences}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pereira, Jordi The robust (minmax regret) assembly line worker assignment and balancing problem Journal Article COMPUTERS & OPERATIONS RESEARCH, 93 , pp. 27-40, 2018, ISSN: 0305-0548. @article{ISI:000427339800003, title = {The robust (minmax regret) assembly line worker assignment and balancing problem}, author = {Jordi Pereira}, doi = {10.1016/j.cor.2018.01.009}, issn = {0305-0548}, year = {2018}, date = {2018-05-01}, journal = {COMPUTERS & OPERATIONS RESEARCH}, volume = {93}, pages = {27-40}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {Line balancing aims to assign the assembly tasks to the stations that compose the assembly line. A recent body of literature has been devoted to heterogeneity in the assembly process introduced by different workers. In such an environment, task times depend on the worker performing the operation and the problem aims at assigning tasks and workers to stations in order to maximize the throughput of the line. In this work, we consider an interval data version of the assembly line worker assignment and balancing problem (ALWABP) in which it is assumed that lower and upper bounds for the task times are known, and the objective is to find an assignment of tasks and workers to the workstations such that the absolute maximum regret among all of the possible scenarios is minimized. The relationship with other interval data minmax regret (IDMR) problems is investigated, the inapplicability of previous approximation methods is studied, regret evaluation is considered, and exact and heuristic solution methods are proposed and analyzed. The results of the proposed methods are compared in a computational experiment, showing the applicability of the method and the theoretical results to solve the problem under study. Additionally, these results are not only applicable to the problem in hand, but also to a more general class of problems. (C) 2018 Elsevier Ltd. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Line balancing aims to assign the assembly tasks to the stations that compose the assembly line. A recent body of literature has been devoted to heterogeneity in the assembly process introduced by different workers. In such an environment, task times depend on the worker performing the operation and the problem aims at assigning tasks and workers to stations in order to maximize the throughput of the line. In this work, we consider an interval data version of the assembly line worker assignment and balancing problem (ALWABP) in which it is assumed that lower and upper bounds for the task times are known, and the objective is to find an assignment of tasks and workers to the workstations such that the absolute maximum regret among all of the possible scenarios is minimized. The relationship with other interval data minmax regret (IDMR) problems is investigated, the inapplicability of previous approximation methods is studied, regret evaluation is considered, and exact and heuristic solution methods are proposed and analyzed. The results of the proposed methods are compared in a computational experiment, showing the applicability of the method and the theoretical results to solve the problem under study. Additionally, these results are not only applicable to the problem in hand, but also to a more general class of problems. (C) 2018 Elsevier Ltd. All rights reserved. |
Bozkurt, D; Rondanelli, R; í, Mar J C; Garreaud, R Foehn Event Triggered by an Atmospheric River Underlies Record-Setting Temperature Along Continental Antarctica Journal Article Journal of Geophysical Research: Atmospheres, 123 (8), pp. 3871–3892, 2018. @article{Bozkurt2018, title = {Foehn Event Triggered by an Atmospheric River Underlies Record-Setting Temperature Along Continental Antarctica}, author = {D Bozkurt and R Rondanelli and Mar J C \'{i} and R Garreaud}, url = {https://doi.org/10.1002/2017jd027796}, doi = {10.1002/2017jd027796}, year = {2018}, date = {2018-04-01}, journal = {Journal of Geophysical Research: Atmospheres}, volume = {123}, number = {8}, pages = {3871--3892}, publisher = {American Geophysical Union (AGU)}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Rojas-Nunez, J; Gonzalez, R I; Bringa, E M; Allende, S; Sepúlveda, P; Arancibia-Miranda, N; Baltazar, S E Toward Controlled Morphology of FeCu Nanoparticles: Cu Concentration and Size Effects Journal Article Journal of Physical Chemistry C, 122 (15), 2018, ISSN: 19327455. @article{rojas-nunez_toward_2018, title = {Toward Controlled Morphology of FeCu Nanoparticles: Cu Concentration and Size Effects}, author = {J Rojas-Nunez and R I Gonzalez and E M Bringa and S Allende and P Sep\'{u}lveda and N Arancibia-Miranda and S E Baltazar}, doi = {10.1021/acs.jpcc.7b11556}, issn = {19327455}, year = {2018}, date = {2018-01-01}, journal = {Journal of Physical Chemistry C}, volume = {122}, number = {15}, abstract = {© 2018 American Chemical Society. Bimetallic nanoparticles (NPs) can be tailored by varying the concentration of their constituent elements, resulting in novel structures and/or configurations, leading to interesting electronic, mechanical, and chemical properties. In this paper, by means of molecular dynamics calculations, we study the morphology of bimetallic FeCu NPs as a function of the Cu concentration. Our results evidence a core-shell (CS) structure for low Cu concentrations and a Janus (JN)-like morphology for high Cu content. Structural and energy characterizations were performed to determine the atomic-scale behavior of the NPs. Using a continuous model to describe immiscible components, we obtain a stability transition curve between CS and JN-like structures for several NP sizes and concentrations. Results from both methods are compared with experimental data obtained for NPs with low and high Cu content, evidencing a good agreement among the three approaches.}, keywords = {}, pubstate = {published}, tppubtype = {article} } © 2018 American Chemical Society. Bimetallic nanoparticles (NPs) can be tailored by varying the concentration of their constituent elements, resulting in novel structures and/or configurations, leading to interesting electronic, mechanical, and chemical properties. In this paper, by means of molecular dynamics calculations, we study the morphology of bimetallic FeCu NPs as a function of the Cu concentration. Our results evidence a core-shell (CS) structure for low Cu concentrations and a Janus (JN)-like morphology for high Cu content. Structural and energy characterizations were performed to determine the atomic-scale behavior of the NPs. Using a continuous model to describe immiscible components, we obtain a stability transition curve between CS and JN-like structures for several NP sizes and concentrations. Results from both methods are compared with experimental data obtained for NPs with low and high Cu content, evidencing a good agreement among the three approaches. |
Córdoba, Andrés The Effects of the Interplay between Motor and Brownian Forces on the Rheology of Active Gels Journal Article Journal of Physical Chemistry C, pp. 11, 2018. @article{cordoba_effects_2018, title = {The Effects of the Interplay between Motor and Brownian Forces on the Rheology of Active Gels}, author = {Andr\'{e}s C\'{o}rdoba}, doi = {10.1021/acs.jpcb.8b00238}, year = {2018}, date = {2018-01-01}, journal = {Journal of Physical Chemistry C}, pages = {11}, abstract = {Active gels perform key mechanical roles inside the cell, such as cell division, motion, and force sensing. The unique mechanical properties required to perform such functions arise from the interactions between molecular motors and semiflexible polymeric filaments. Molecular motors can convert the energy released in the hydrolysis of ATP into forces of up to piconewton magnitudes. Moreover, the polymeric filaments that form active gels are flexible enough to respond to Brownian forces but also stiff enough to support the large tensions induced by the motor-generated forces. Brownian forces are expected to have a significant effect especially at motor activities at which stable noncontractile in vitro active gels are prepared for rheological measurements. Here, a microscopic mean-field theory of active gels originally formulated in the limit of motor-dominated dynamics is extended to include Brownian forces. In the model presented here, Brownian forces are included accurately, at real room temperature, even in systems with high motor activity. It is shown that a subtle interplay, or competition, between motor-generated forces and Brownian forces has an important impact on the mass transport and rheological properties of active gels. The model predictions show that at low frequencies the dynamic modulus of active gels is determined mostly by motor protein dynamics. However, Brownian forces significantly increase the breadth of the relaxation spectrum and can affect the shape of the dynamic modulus over a wide frequency range even for ratios of motor to Brownian forces of more than a hundred. Since the ratio between motor and Brownian forces is sensitive to ATP concentration, the results presented here shed some light on how the transient mechanical response of active gels changes with varying ATP concentration.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Active gels perform key mechanical roles inside the cell, such as cell division, motion, and force sensing. The unique mechanical properties required to perform such functions arise from the interactions between molecular motors and semiflexible polymeric filaments. Molecular motors can convert the energy released in the hydrolysis of ATP into forces of up to piconewton magnitudes. Moreover, the polymeric filaments that form active gels are flexible enough to respond to Brownian forces but also stiff enough to support the large tensions induced by the motor-generated forces. Brownian forces are expected to have a significant effect especially at motor activities at which stable noncontractile in vitro active gels are prepared for rheological measurements. Here, a microscopic mean-field theory of active gels originally formulated in the limit of motor-dominated dynamics is extended to include Brownian forces. In the model presented here, Brownian forces are included accurately, at real room temperature, even in systems with high motor activity. It is shown that a subtle interplay, or competition, between motor-generated forces and Brownian forces has an important impact on the mass transport and rheological properties of active gels. The model predictions show that at low frequencies the dynamic modulus of active gels is determined mostly by motor protein dynamics. However, Brownian forces significantly increase the breadth of the relaxation spectrum and can affect the shape of the dynamic modulus over a wide frequency range even for ratios of motor to Brownian forces of more than a hundred. Since the ratio between motor and Brownian forces is sensitive to ATP concentration, the results presented here shed some light on how the transient mechanical response of active gels changes with varying ATP concentration. |
Riquelme, Jorge; Neira, Karinna; Marco, José F; Hermosilla-Ibáñez, Patricio; Venegas-Yazigi, Diego; Orellana, Walter; Ponce, Ingrid; Zagal, José H; Tasca, Federico Transactions, E C S Society, The Electrochemical, 85 (12), pp. 111–121, 2018. @article{riquelme_climbing_2018, title = {Climbing Over the Activity Volcano Correlation By Biomimicking Vitamin B12: A Co Phthalocyanine Pyridine Axial Ligand Coordinated Catalyst for the Reduction of Molecular Oxygen Jorge Riquelme,}, author = {Jorge Riquelme and Karinna Neira and Jos\'{e} F Marco and Patricio Hermosilla-Ib\'{a}\~{n}ez and Diego Venegas-Yazigi and Walter Orellana and Ingrid Ponce and Jos\'{e} H Zagal and Federico Tasca}, doi = {10.1149/08512.0111ecst}, year = {2018}, date = {2018-01-01}, journal = {Transactions, E C S Society, The Electrochemical}, volume = {85}, number = {12}, pages = {111--121}, abstract = {CoN4 macrocyclic complexes like Co phthalocyanines (CoPc) have been extensively studied as electrocatalysts for the ORR but they preferentially promote the 2-e reduction of O2 to give peroxide. In contrast, vitamin B12, a naturally occurring CoN4 macrocyclic molecule alkaline media promotes the 4-electron reduction of O2 to H2O. Vitamin B12 possesses an imidazole axial back ligand and this seems to be the reason for its higher activity and selectivity for the 4-e reduction of O2. To test this hypothesis, we synthesized a CoPc axially coordinated to pyridine anchored to carbon nanotubes (Co-Py-CNT). The Co center is therefore coordinated to 5 nitrogens as in vitamin B12. The modified CoPcPy containing catalytic material was characterized by EPR and XPS spectroscopy. DFT calculations. According to our results the pyridine back ligand increases the Co-O2 binding energy, making it more similar to VitB12, favoring the splitting of the O-O bond. The back ligand then plays a crucial role in modifying Co- O2 binding energy which is a well know reactivity descriptor. A further evidence of this dramatic change in reactivity of CoPc by the presence of the "Py" back ligand is that it moves from the weak binding leg of a volcano correlation to the strong leg of the volcano. This might explain why nature uses a back ligand in cytochrome c to catalyze the ORR.}, keywords = {}, pubstate = {published}, tppubtype = {article} } CoN4 macrocyclic complexes like Co phthalocyanines (CoPc) have been extensively studied as electrocatalysts for the ORR but they preferentially promote the 2-e reduction of O2 to give peroxide. In contrast, vitamin B12, a naturally occurring CoN4 macrocyclic molecule alkaline media promotes the 4-electron reduction of O2 to H2O. Vitamin B12 possesses an imidazole axial back ligand and this seems to be the reason for its higher activity and selectivity for the 4-e reduction of O2. To test this hypothesis, we synthesized a CoPc axially coordinated to pyridine anchored to carbon nanotubes (Co-Py-CNT). The Co center is therefore coordinated to 5 nitrogens as in vitamin B12. The modified CoPcPy containing catalytic material was characterized by EPR and XPS spectroscopy. DFT calculations. According to our results the pyridine back ligand increases the Co-O2 binding energy, making it more similar to VitB12, favoring the splitting of the O-O bond. The back ligand then plays a crucial role in modifying Co- O2 binding energy which is a well know reactivity descriptor. A further evidence of this dramatic change in reactivity of CoPc by the presence of the "Py" back ligand is that it moves from the weak binding leg of a volcano correlation to the strong leg of the volcano. This might explain why nature uses a back ligand in cytochrome c to catalyze the ORR. |
Hart, Andrew; Cortés, María Paz; Latorre, Mauricio; Martinez, Servet Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium Journal Article PLOS ONE, 13 (5), pp. 1–17, 2018. @article{hart_codon_2018, title = {Codon usage bias reveals genomic adaptations to environmental conditions in an acidophilic consortium}, author = {Andrew Hart and Mar\'{i}a Paz Cort\'{e}s and Mauricio Latorre and Servet Martinez}, url = {https://doi.org/10.1371/journal.pone.0195869}, doi = {10.1371/journal.pone.0195869}, year = {2018}, date = {2018-01-01}, journal = {PLOS ONE}, volume = {13}, number = {5}, pages = {1--17}, abstract = {The analysis of codon usage bias has been widely used to characterize different communities of microorganisms. In this context, the aim of this work was to study the codon usage bias in a natural consortium of five acidophilic bacteria used for biomining. The codon usage bias of the consortium was contrasted with genes from an alternative collection of acidophilic reference strains and metagenome samples. Results indicate that acidophilic bacteria preferentially have low codon usage bias, consistent with both their capacity to live in a wide range of habitats and their slow growth rate, a characteristic probably acquired independently from their phylogenetic relationships. In addition, the analysis showed significant differences in the unique sets of genes from the autotrophic species of the consortium in relation to other acidophilic organisms, principally in genes which code for proteins involved in metal and oxidative stress resistance. The lower values of codon usage bias obtained in this unique set of genes suggest higher transcriptional adaptation to living in extreme conditions, which was probably acquired as a measure for resisting the elevated metal conditions present in the mine.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The analysis of codon usage bias has been widely used to characterize different communities of microorganisms. In this context, the aim of this work was to study the codon usage bias in a natural consortium of five acidophilic bacteria used for biomining. The codon usage bias of the consortium was contrasted with genes from an alternative collection of acidophilic reference strains and metagenome samples. Results indicate that acidophilic bacteria preferentially have low codon usage bias, consistent with both their capacity to live in a wide range of habitats and their slow growth rate, a characteristic probably acquired independently from their phylogenetic relationships. In addition, the analysis showed significant differences in the unique sets of genes from the autotrophic species of the consortium in relation to other acidophilic organisms, principally in genes which code for proteins involved in metal and oxidative stress resistance. The lower values of codon usage bias obtained in this unique set of genes suggest higher transcriptional adaptation to living in extreme conditions, which was probably acquired as a measure for resisting the elevated metal conditions present in the mine. |
Slater, Paula G; Gutierrez-Maldonado, Sebastian E; Gysling, Katia; Lagos, Carlos F Molecular modeling of structures and interaction of human corticotropin-releasing factor (CRF) binding protein and CRF Type-2 receptor Journal Article Frontiers in Endocrinology, 9 (FEB), pp. 1–14, 2018, ISSN: 16642392. @article{slater_molecular_2018, title = {Molecular modeling of structures and interaction of human corticotropin-releasing factor (CRF) binding protein and CRF Type-2 receptor}, author = {Paula G Slater and Sebastian E Gutierrez-Maldonado and Katia Gysling and Carlos F Lagos}, doi = {10.3389/fendo.2018.00043}, issn = {16642392}, year = {2018}, date = {2018-01-01}, journal = {Frontiers in Endocrinology}, volume = {9}, number = {FEB}, pages = {1--14}, abstract = {The corticotropin-releasing factor (CRF) system is a key mediator of the stress response and addictive behavior. The CRF system includes four peptides: The CRF system includes four peptides: CRF, urocortins I-III, CRF binding protein (CRF-BP) that binds CRF with high affinity, and two class B G-protein coupled receptors CRF1R and CRF2R. CRF-BP is a secreted protein without significant sequence homology to CRF receptors or to any other known class of protein. Recently, it has been described a potentiation role of CRF-BP over CRF signaling through CRF2R in addictive-related neuronal plasticity and behavior. In addition, it has been described that CRF-BP is capable to physically interact specifically with the α isoform of CRF2R and acts like an escort protein increasing the amount of the receptor in the plasma membrane. At present, there are no available structures for CRF-BP or for full-length CRFR. Knowing and studying the structure of these proteins could be beneficial in order to characterize the CRF-BP/CRF2αR interaction. In this work, we report the modeling of CRF-BP and of full-length CRF2αR and CRF2βR based on the recently solved crystal structures of the transmembrane domains of the human glucagon receptor and human CRF1R, in addition with the resolved N-terminal extracellular domain of CRFRs. These models were further studied using molecular dynamics simulations and protein-protein docking. The results predicted a higher possibility of interaction of CRF-BP with CRF2αR than CRF2βR and yielded the possible residues conforming the interacting interface. Thus, the present study provides a framework for further investigation of the CRF-BP/CRF2αR interaction.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The corticotropin-releasing factor (CRF) system is a key mediator of the stress response and addictive behavior. The CRF system includes four peptides: The CRF system includes four peptides: CRF, urocortins I-III, CRF binding protein (CRF-BP) that binds CRF with high affinity, and two class B G-protein coupled receptors CRF1R and CRF2R. CRF-BP is a secreted protein without significant sequence homology to CRF receptors or to any other known class of protein. Recently, it has been described a potentiation role of CRF-BP over CRF signaling through CRF2R in addictive-related neuronal plasticity and behavior. In addition, it has been described that CRF-BP is capable to physically interact specifically with the α isoform of CRF2R and acts like an escort protein increasing the amount of the receptor in the plasma membrane. At present, there are no available structures for CRF-BP or for full-length CRFR. Knowing and studying the structure of these proteins could be beneficial in order to characterize the CRF-BP/CRF2αR interaction. In this work, we report the modeling of CRF-BP and of full-length CRF2αR and CRF2βR based on the recently solved crystal structures of the transmembrane domains of the human glucagon receptor and human CRF1R, in addition with the resolved N-terminal extracellular domain of CRFRs. These models were further studied using molecular dynamics simulations and protein-protein docking. The results predicted a higher possibility of interaction of CRF-BP with CRF2αR than CRF2βR and yielded the possible residues conforming the interacting interface. Thus, the present study provides a framework for further investigation of the CRF-BP/CRF2αR interaction. |
Suzuki, Kosuke; Aravena, Daniel; Minato, Takuo; Ruiz, Eliseo; Yamaguchi, Kazuya; Mizuno, Noritaka Effect of Heteroatoms on Field-Induced Slow Magnetic Relaxation of Mononuclear FeIII (S = 5/2) Ions within Polyoxometalates Journal Article Inorganic Chemistry, 3 , pp. 2–4, 2018. @article{suzuki_effect_2018, title = {Effect of Heteroatoms on Field-Induced Slow Magnetic Relaxation of Mononuclear FeIII (S = 5/2) Ions within Polyoxometalates}, author = {Kosuke Suzuki and Daniel Aravena and Takuo Minato and Eliseo Ruiz and Kazuya Yamaguchi and Noritaka Mizuno}, doi = {10.1021/acs.inorgchem.8b00644}, year = {2018}, date = {2018-01-01}, journal = {Inorganic Chemistry}, volume = {3}, pages = {2--4}, abstract = {In this paper, the synthesis and magnetic properties of mononuclear FeIII-containing polyoxometalates (POMs) with differ- ent types of heteroatoms, TBA7H10[(A-α-XW9O34)2Fe] (IIX}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this paper, the synthesis and magnetic properties of mononuclear FeIII-containing polyoxometalates (POMs) with differ- ent types of heteroatoms, TBA7H10[(A-α-XW9O34)2Fe] (IIX |
Santana, Ricardo De; Fuentealba, Pablo; Maia, Lauro; Paredes-Garcia, Veronica; Aravena, Daniel; Venegas-Yazigi, Diego; Manzur, Jorge; Spodine, Evgenia Solid state photoluminescence studies of [EuLnH2(NO3)3](Ħ2O)x macrocyclic complexes with Schiff base ligands Journal Article Journal of Luminescence, 2018, ISSN: 0022-2313. @article{de_santana_solid_2018, title = {Solid state photoluminescence studies of [EuLnH2(NO3)3]({H}2O)x macrocyclic complexes with Schiff base ligands}, author = {Ricardo De Santana and Pablo Fuentealba and Lauro Maia and Veronica Paredes-Garcia and Daniel Aravena and Diego Venegas-Yazigi and Jorge Manzur and Evgenia Spodine}, url = {https://doi.org/10.1016/j.jlumin.2018.06.022}, doi = {10.1016/j.jlumin.2018.06.022}, issn = {0022-2313}, year = {2018}, date = {2018-01-01}, journal = {Journal of Luminescence}, abstract = {Three EuIII macrocyclic complexes [EuLnH2(NO3)3](H2O)x based on the ligands derived from 2-hydroxy-5- methyl-1,3-benzenedicarbaldehyde and three different amines: o-phenylenediamine, Eu-OPDA; ethylenedia- mine, Eu-EDA; and 1,3-diaminopropane, Eu-DAP have been synthesized via a metal template reaction. Eu- EDA and Eu-DAP showed metal based emission; for the Eu-OPDA complex these luminescent properties were not observed. From the photoluminescence emission measurements from ∼13 to 300 K, the R/O = I (5D0 → 7F2)/I (5D0 → 7F1) ratio, together with two intensity parameters ($\Omega$2 and $\Omega$4), radiative lifetimes (τR) and branching ratios (β0 J′) were calculated based on the Judd-Ofelt theory, for Eu-EDA and Eu-DAP. While the behavior of these parameters for the Eu-DAP complex is temperature dependent, these remain constant for Eu- EDA. The temperature dependence observed for the Eu-DAP complex indicates that for temperatures below 120 K, the local symmetry of the EuIII center is modified, as compared to the environment of the same metal center at room temperature.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Three EuIII macrocyclic complexes [EuLnH2(NO3)3](H2O)x based on the ligands derived from 2-hydroxy-5- methyl-1,3-benzenedicarbaldehyde and three different amines: o-phenylenediamine, Eu-OPDA; ethylenedia- mine, Eu-EDA; and 1,3-diaminopropane, Eu-DAP have been synthesized via a metal template reaction. Eu- EDA and Eu-DAP showed metal based emission; for the Eu-OPDA complex these luminescent properties were not observed. From the photoluminescence emission measurements from ∼13 to 300 K, the R/O = I (5D0 → 7F2)/I (5D0 → 7F1) ratio, together with two intensity parameters ($Ømega$2 and $Ømega$4), radiative lifetimes (τR) and branching ratios (β0 J′) were calculated based on the Judd-Ofelt theory, for Eu-EDA and Eu-DAP. While the behavior of these parameters for the Eu-DAP complex is temperature dependent, these remain constant for Eu- EDA. The temperature dependence observed for the Eu-DAP complex indicates that for temperatures below 120 K, the local symmetry of the EuIII center is modified, as compared to the environment of the same metal center at room temperature. |
Xiang, Yuan; Camarada, María Belén; Wen, Yangping; Wu, Hao; Chen, Jinyin; Li, Mingfang; Liao, Xiaoning Simple voltammetric analyses of ochratoxin A in food samples using highly-stable and anti-fouling black phosphorene nanosensor Journal Article Electrochimica Acta, 282 , pp. 490–498, 2018, ISSN: 00134686. @article{xiang_simple_2018, title = {Simple voltammetric analyses of ochratoxin A in food samples using highly-stable and anti-fouling black phosphorene nanosensor}, author = {Yuan Xiang and Mar\'{i}a Bel\'{e}n Camarada and Yangping Wen and Hao Wu and Jinyin Chen and Mingfang Li and Xiaoning Liao}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0013468618313434}, doi = {10.1016/j.electacta.2018.06.055}, issn = {00134686}, year = {2018}, date = {2018-01-01}, journal = {Electrochimica Acta}, volume = {282}, pages = {490--498}, abstract = {There are few reports on the electrochemical detection of ochratoxin A (OTA) using chemically modified electrode owing to the OTA poor electrochemical activity and strong fouling effect towards electrode surface. In this study, a novel nanosensor based on two-dimensional (2D) layered black phosphorene (BP) was successfully developed for the simple voltammetric detection of OTA in grape juice and red wine samples. The BP modified nanosensor showed a good linear electrochemical response towards OTA in a concentration range of 0.3\textendash10 μg/mL with a detection limit of 0.18 μg/mL (S/N = 3) under the optimal conditions. A mechanism for the electrocatalytic oxidation of OTA was proposed and verified by density functional theory calculations that the oxidation of OTA is an irreversible electrochemical response with an adsorption-controlled process, and the nitrogen atom of the amide is oxidized to N+O− with two protons and two electrons. The proposed electrochemical sensor demonstrated good electrochemical stability, superior anti-fouling property and excellent sensitivity towards OTA detection. A satisfactory practicability with recoveries between 98.8% and 103.3% was obtained in real samples determination. This work puts forward a new sensing platform based on the two-dimensional layered graphene-like nanosensor for the electrochemical determination of mycotoxins in edible agricultural food.}, keywords = {}, pubstate = {published}, tppubtype = {article} } There are few reports on the electrochemical detection of ochratoxin A (OTA) using chemically modified electrode owing to the OTA poor electrochemical activity and strong fouling effect towards electrode surface. In this study, a novel nanosensor based on two-dimensional (2D) layered black phosphorene (BP) was successfully developed for the simple voltammetric detection of OTA in grape juice and red wine samples. The BP modified nanosensor showed a good linear electrochemical response towards OTA in a concentration range of 0.3–10 μg/mL with a detection limit of 0.18 μg/mL (S/N = 3) under the optimal conditions. A mechanism for the electrocatalytic oxidation of OTA was proposed and verified by density functional theory calculations that the oxidation of OTA is an irreversible electrochemical response with an adsorption-controlled process, and the nitrogen atom of the amide is oxidized to N+O− with two protons and two electrons. The proposed electrochemical sensor demonstrated good electrochemical stability, superior anti-fouling property and excellent sensitivity towards OTA detection. A satisfactory practicability with recoveries between 98.8% and 103.3% was obtained in real samples determination. This work puts forward a new sensing platform based on the two-dimensional layered graphene-like nanosensor for the electrochemical determination of mycotoxins in edible agricultural food. |
Contreras, Antonio V; Llanes, Antonio; Pérez-Bernabeu, Alberto; Navarro, Sergio; Pérez-Sánchez, Horacio; López-Espín, Jose J; Cecilia, José M ENMX: An elastic network model to predict the FOREX market evolution Journal Article Simulation Modelling Practice and Theory, 86 (April), pp. 1–10, 2018, ISSN: 1569190X. @article{contreras_enmx:_2018, title = {ENMX: An elastic network model to predict the FOREX market evolution}, author = {Antonio V Contreras and Antonio Llanes and Alberto P\'{e}rez-Bernabeu and Sergio Navarro and Horacio P\'{e}rez-S\'{a}nchez and Jose J L\'{o}pez-Esp\'{i}n and Jos\'{e} M Cecilia}, url = {https://doi.org/10.1016/j.simpat.2018.04.008}, doi = {10.1016/j.simpat.2018.04.008}, issn = {1569190X}, year = {2018}, date = {2018-01-01}, journal = {Simulation Modelling Practice and Theory}, volume = {86}, number = {April}, pages = {1--10}, abstract = {The foreign exchange (FOREX) market is a financial market in which participants, such as international banks, companies or private investors, can both invest in and speculate on exchange rates. This market is considered one of the largest financial markets in the world in terms of trading volume. Indeed, the just-in-time price prediction for a currency pair exchange rate (e.g. EUR/USD) provides valuable information for companies and investors as they can take different actions to improve their business. This paper introduces a new algorithm, inspired by the behaviour of macromolecules in dissolution, to model the evolution of the FOREX market, called the ENMX (elastic network model for FOREX market) algorithm. This algorithm allows the system to escape from a potential local minimum, so it can reproduce the unstable nature of the FOREX market, allowing the simulation to get away from equilibrium. ENMX introduces several novelties in the simulation of the FOREX market. First, ENMX enables the user to simulate the market evolution of up to 21 currency pairs, connected, and thus emulating behaviour of the real-world FOREX market. Second, the interaction between investors and each particular quotation, which may introduce slight deviations from the quotation prices, is represented by a random movement. We analyse different probability distributions like Gaussian and Pseudo-Voigt, the latter showing better behaviour distributions, to model the variations in quotation prices. Finally, the ENMX algorithm is also compared to traditional econometric approaches such as the VAR model and a driftless random walk, using a classical statistical and a profitability measure. The results show that the ENMX outperforms both models in terms of quality by a wide margin.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The foreign exchange (FOREX) market is a financial market in which participants, such as international banks, companies or private investors, can both invest in and speculate on exchange rates. This market is considered one of the largest financial markets in the world in terms of trading volume. Indeed, the just-in-time price prediction for a currency pair exchange rate (e.g. EUR/USD) provides valuable information for companies and investors as they can take different actions to improve their business. This paper introduces a new algorithm, inspired by the behaviour of macromolecules in dissolution, to model the evolution of the FOREX market, called the ENMX (elastic network model for FOREX market) algorithm. This algorithm allows the system to escape from a potential local minimum, so it can reproduce the unstable nature of the FOREX market, allowing the simulation to get away from equilibrium. ENMX introduces several novelties in the simulation of the FOREX market. First, ENMX enables the user to simulate the market evolution of up to 21 currency pairs, connected, and thus emulating behaviour of the real-world FOREX market. Second, the interaction between investors and each particular quotation, which may introduce slight deviations from the quotation prices, is represented by a random movement. We analyse different probability distributions like Gaussian and Pseudo-Voigt, the latter showing better behaviour distributions, to model the variations in quotation prices. Finally, the ENMX algorithm is also compared to traditional econometric approaches such as the VAR model and a driftless random walk, using a classical statistical and a profitability measure. The results show that the ENMX outperforms both models in terms of quality by a wide margin. |
Moreno, Felipe; Davis, Sergio; Loyola, Claudia; Peralta, Joaquín Ordered metastable states in the Potts model and their connection with the superheated solid state Journal Article Physica A: Statistical Mechanics and its Applications, 509 , pp. 361 – 368, 2018, ISSN: 0378-4371. @article{moreno_ordered_2018, title = {Ordered metastable states in the Potts model and their connection with the superheated solid state}, author = {Felipe Moreno and Sergio Davis and Claudia Loyola and Joaqu\'{i}n Peralta}, url = {http://www.sciencedirect.com/science/article/pii/S0378437118307301}, doi = {https://doi.org/10.1016/j.physa.2018.06.006}, issn = {0378-4371}, year = {2018}, date = {2018-01-01}, journal = {Physica A: Statistical Mechanics and its Applications}, volume = {509}, pages = {361 -- 368}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Ríos-González, J A; Menéndez-Proupin, E; Peña, J L Theoretical study of bismuth-doped CdTe Journal Article Journal of Physics: Conference Series, 1043 (1), pp. 012044, 2018. @article{1742-6596-1043-1-012044, title = {Theoretical study of bismuth-doped CdTe}, author = {J A R\'{i}os-Gonz\'{a}lez and E Men\'{e}ndez-Proupin and J L Pe\~{n}a}, url = {http://stacks.iop.org/1742-6596/1043/i=1/a=012044}, year = {2018}, date = {2018-01-01}, journal = {Journal of Physics: Conference Series}, volume = {1043}, number = {1}, pages = {012044}, abstract = {The electronic structure and thermodynamic properties of bismuth impurities in cadmium telluride (CdTe) are studied by means density functional theory calculations. The exchange and correlation are treated using the hybrid functional HSE, where the range-separation parameter is tuned to fit the CdTe band gap. The spin-orbit coupling is included in the calculations, showing a strong effect on the Bi-related energy levels. The band diagram and the formation energies are obtained for substitutional and interstitial configurations. It is shown that simple substitutional impurities can generate in-gap bands, which can act as intermediate levels in two-photon absorption and can be appropriate for intermediate-band solar cells.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The electronic structure and thermodynamic properties of bismuth impurities in cadmium telluride (CdTe) are studied by means density functional theory calculations. The exchange and correlation are treated using the hybrid functional HSE, where the range-separation parameter is tuned to fit the CdTe band gap. The spin-orbit coupling is included in the calculations, showing a strong effect on the Bi-related energy levels. The band diagram and the formation energies are obtained for substitutional and interstitial configurations. It is shown that simple substitutional impurities can generate in-gap bands, which can act as intermediate levels in two-photon absorption and can be appropriate for intermediate-band solar cells. |
Casanova-Páez, M; Menéndez-Proupin, E Density functional theory study of defects in cadmium telluride: a PBC and QM/MM comparison Journal Article Journal of Physics: Conference Series, 1043 (1), pp. 012043, 2018. @article{1742-6596-1043-1-012043, title = {Density functional theory study of defects in cadmium telluride: a PBC and QM/MM comparison}, author = {M Casanova-P\'{a}ez and E Men\'{e}ndez-Proupin}, url = {http://stacks.iop.org/1742-6596/1043/i=1/a=012043}, year = {2018}, date = {2018-01-01}, journal = {Journal of Physics: Conference Series}, volume = {1043}, number = {1}, pages = {012043}, abstract = {Ab initio calculations, in the framework of density functional theory (DFT), are employed to determine the formation energies of tellurium vacancy (VTe) for different ionized states. We performed a periodic boundary conditions (PBC) calculation, applying quasiparticle corrections and establishing the thermodynamic transition level. In addition, we have also used the quantum mechanics/molecular mechanics (QM/MM) approach in order to check its capability predicting formation energies, finding similar results compared to the previous supercell method.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Ab initio calculations, in the framework of density functional theory (DFT), are employed to determine the formation energies of tellurium vacancy (VTe) for different ionized states. We performed a periodic boundary conditions (PBC) calculation, applying quasiparticle corrections and establishing the thermodynamic transition level. In addition, we have also used the quantum mechanics/molecular mechanics (QM/MM) approach in order to check its capability predicting formation energies, finding similar results compared to the previous supercell method. |
Povea, Paula; Arroyo, Juan Luis; Carreño, Gustavo; Norambuena, Ángel; Rios, Paulina L; Camarada, Maria Belen; Chavez, Ivonne; Manriquez, Juan Manuel; Morales-Verdejo, Cesar Thermochimica Acta, 2018, ISSN: 0040-6031. @article{POVEA2018, title = {Catalytic effects of p-Phenylene-Bridged Methylated Binuclear Ferrocenes on thermal decomposition of the main component of composite solid propellants}, author = {Paula Povea and Juan Luis Arroyo and Gustavo Carre\~{n}o and \'{A}ngel Norambuena and Paulina L Rios and Maria Belen Camarada and Ivonne Chavez and Juan Manuel Manriquez and Cesar Morales-Verdejo}, url = {http://www.sciencedirect.com/science/article/pii/S0040603118304568}, doi = {https://doi.org/10.1016/j.tca.2018.06.020}, issn = {0040-6031}, year = {2018}, date = {2018-01-01}, journal = {Thermochimica Acta}, abstract = {This contribution describes the catalytic activity of homobimetallic complexes derived from p-phenylene on the thermal decomposition of ammonium perchlorate (abbreviated as AP). The complexes, [CpFe-p-Ph-FeCp] (1), [Cp*Fe-p-Ph-FeCp*] (2), [CpFe-p-Ph’-FeCp] (3) and [Cp*Fe-p-Ph’-FeCp*] (4) (with p-Ph: p-Bis(3,4-dimethylcyclopentadienyl)benzene and p-Ph’: p-Bis(2,3,4,5-tetramethylcyclopentadienyl)benzene), were compared with the catalytic activity of the catocene (cat) complex previously reported. Furthermore, in order to clarify the mechanism of the bimetallic compounds, it was tested ferrocene (Fc), frequently used as burning rate (BR) catalyst on the thermal decomposition of AP. The synthetized compounds shown a shift on the peak temperature to lower values and an increase in the released heats during thermal decomposition of AP. The burning rate catalytic activity of the compounds on thermal decomposition of AP were examined by thermogravimetry and differential scanning calorimetry techniques. Theoretical calculations of these compounds were carried out to gain further understanding of these catalysts systems.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This contribution describes the catalytic activity of homobimetallic complexes derived from p-phenylene on the thermal decomposition of ammonium perchlorate (abbreviated as AP). The complexes, [CpFe-p-Ph-FeCp] (1), [Cp*Fe-p-Ph-FeCp*] (2), [CpFe-p-Ph’-FeCp] (3) and [Cp*Fe-p-Ph’-FeCp*] (4) (with p-Ph: p-Bis(3,4-dimethylcyclopentadienyl)benzene and p-Ph’: p-Bis(2,3,4,5-tetramethylcyclopentadienyl)benzene), were compared with the catalytic activity of the catocene (cat) complex previously reported. Furthermore, in order to clarify the mechanism of the bimetallic compounds, it was tested ferrocene (Fc), frequently used as burning rate (BR) catalyst on the thermal decomposition of AP. The synthetized compounds shown a shift on the peak temperature to lower values and an increase in the released heats during thermal decomposition of AP. The burning rate catalytic activity of the compounds on thermal decomposition of AP were examined by thermogravimetry and differential scanning calorimetry techniques. Theoretical calculations of these compounds were carried out to gain further understanding of these catalysts systems. |
Karna, Nabin Kumar; Crisson, Andres Rojano; Wagemann, Enrique; Walther, Jens H; Zambrano, Harvey A Effect of an external electric field on capillary filling of water in hydrophilic silica nanochannels Journal Article Phys. Chem. Chem. Phys., pp. -, 2018. @article{C8CP03186J, title = {Effect of an external electric field on capillary filling of water in hydrophilic silica nanochannels}, author = {Nabin Kumar Karna and Andres Rojano Crisson and Enrique Wagemann and Jens H Walther and Harvey A Zambrano}, url = {http://dx.doi.org/10.1039/C8CP03186J}, doi = {10.1039/C8CP03186J}, year = {2018}, date = {2018-01-01}, journal = {Phys. Chem. Chem. Phys.}, pages = {-}, publisher = {The Royal Society of Chemistry}, abstract = {Development of functional nanofluidic devices requires understanding the fundamentals of capillary driven flow in nanochannels. In this context, we conduct molecular dynamics simulations of water capillary imbibition in silica nanoslits under externally applied electric (E) fields with strengths between 0 and 1 V nm-1. For increasing E-fields, we observe a systematic lowering in the meniscus contact angle and a decrease in the corresponding water filling rates. These results contrast markedly the classical Washburn-Bosanquet's equation which predicts an increase in filling rates for lower water contact angles. Our study provides evidence that the observed decrease in water filling rates can be attributed to the interplay between two underlying mechanisms, a reduced fluidity of interfacial water and a systematic alignment of the water molecules in the bulk as a response to the particular strength of the applied E-field. Therefore, during water capillary filling a constant E-field applied in the direction parallel to the water imbibition leads to a lower than expected filling rate caused by a viscosity increase in the bulk and an altered solid-liquid friction on the channel walls. These coupled mechanisms governing capillarity under the action of applied E-fields could be manipulated for controlling imbibition of polar liquid solutions in nanofluidic devices.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Development of functional nanofluidic devices requires understanding the fundamentals of capillary driven flow in nanochannels. In this context, we conduct molecular dynamics simulations of water capillary imbibition in silica nanoslits under externally applied electric (E) fields with strengths between 0 and 1 V nm-1. For increasing E-fields, we observe a systematic lowering in the meniscus contact angle and a decrease in the corresponding water filling rates. These results contrast markedly the classical Washburn-Bosanquet's equation which predicts an increase in filling rates for lower water contact angles. Our study provides evidence that the observed decrease in water filling rates can be attributed to the interplay between two underlying mechanisms, a reduced fluidity of interfacial water and a systematic alignment of the water molecules in the bulk as a response to the particular strength of the applied E-field. Therefore, during water capillary filling a constant E-field applied in the direction parallel to the water imbibition leads to a lower than expected filling rate caused by a viscosity increase in the bulk and an altered solid-liquid friction on the channel walls. These coupled mechanisms governing capillarity under the action of applied E-fields could be manipulated for controlling imbibition of polar liquid solutions in nanofluidic devices. |
Narum, Shawn R; Genova, Alex Di; Micheletti, Steven J; Maass, Alejandro Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon Journal Article Proceedings of the Royal Society B: Biological Sciences, 285 (1883), pp. 20180935, 2018, ISSN: 0962-8452. @article{narum_genomic_2018, title = {Genomic variation underlying complex life-history traits revealed by genome sequencing in Chinook salmon}, author = {Shawn R Narum and Alex Di Genova and Steven J Micheletti and Alejandro Maass}, url = {http://rspb.royalsocietypublishing.org/lookup/doi/10.1098/rspb.2018.0935}, doi = {10.1098/rspb.2018.0935}, issn = {0962-8452}, year = {2018}, date = {2018-01-01}, journal = {Proceedings of the Royal Society B: Biological Sciences}, volume = {285}, number = {1883}, pages = {20180935}, abstract = {A broad portfolio of phenotypic diversity in natural organisms can buffer against exploitation and increase species persistence in disturbed ecosystems. The study of genomic variation that accounts for ecological and evolutionary adaptation can represent a powerful approach to extend understanding of phenotypic variation in nature. Here we present a chromosome-level reference genome assembly for Chinook salmon ( Oncorhynchus tshawytscha ; 2.36 Gb) that enabled association mapping of life-history variation and phenotypic traits for this species. Whole-genome re-sequencing of populations with distinct life-history traits provided evidence that divergent selection was extensive throughout the genome within and among phylogenetic lineages, indicating that a broad portfolio of phenotypic diversity exists in this species that is related to local adaptation and life-history variation. Association mapping with millions of genome-wide SNPs revealed that a genomic region of major effect on chromosome 28 was associated with phenotypes for premature and mature arrival to spawning grounds and was consistent across three distinct phylogenetic lineages. Our results demonstrate how genomic resources can enlighten the genetic basis of known phenotypes in exploited species and assist in clarifying phenotypic variation that may be difficult to observe in naturally occurring organisms.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A broad portfolio of phenotypic diversity in natural organisms can buffer against exploitation and increase species persistence in disturbed ecosystems. The study of genomic variation that accounts for ecological and evolutionary adaptation can represent a powerful approach to extend understanding of phenotypic variation in nature. Here we present a chromosome-level reference genome assembly for Chinook salmon ( Oncorhynchus tshawytscha ; 2.36 Gb) that enabled association mapping of life-history variation and phenotypic traits for this species. Whole-genome re-sequencing of populations with distinct life-history traits provided evidence that divergent selection was extensive throughout the genome within and among phylogenetic lineages, indicating that a broad portfolio of phenotypic diversity exists in this species that is related to local adaptation and life-history variation. Association mapping with millions of genome-wide SNPs revealed that a genomic region of major effect on chromosome 28 was associated with phenotypes for premature and mature arrival to spawning grounds and was consistent across three distinct phylogenetic lineages. Our results demonstrate how genomic resources can enlighten the genetic basis of known phenotypes in exploited species and assist in clarifying phenotypic variation that may be difficult to observe in naturally occurring organisms. |
Genova, Alex Di; Ruz, Gonzalo A; Sagot, Marie-France; Maass, Alejandro Fast-SG: an alignment-free algorithm for hybrid assembly Journal Article GigaScience, 7 (5), pp. giy048, 2018. @article{di_genova_fast-sg:_2018, title = {Fast-SG: an alignment-free algorithm for hybrid assembly}, author = {Alex Di Genova and Gonzalo A Ruz and Marie-France Sagot and Alejandro Maass}, url = {http://dx.doi.org/10.1093/gigascience/giy048}, doi = {10.1093/gigascience/giy048}, year = {2018}, date = {2018-01-01}, journal = {GigaScience}, volume = {7}, number = {5}, pages = {giy048}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Mazzeo, Andrea; Huneeus, Nicolás; Ordoñez, César; Orfanoz-Cheuquelaf, Andrea; Menut, Laurent; Mailler, Sylvan; Valari, Myrto; van der Gon, Hugo Denier; Gallardo, Laura; Muñoz, Ricardo; Donoso, Rodrigo; Galleguillos, Maurico; Osses, Mauricio; Tolvett, Sebastian Impact of residential combustion and transport emissions on air pollution in Santiago during winter Journal Article Atmospheric Environment, 190 , pp. 195 – 208, 2018, ISSN: 1352-2310. @article{mazzeo_impact_2018, title = {Impact of residential combustion and transport emissions on air pollution in Santiago during winter}, author = {Andrea Mazzeo and Nicol\'{a}s Huneeus and C\'{e}sar Ordo\~{n}ez and Andrea Orfanoz-Cheuquelaf and Laurent Menut and Sylvan Mailler and Myrto Valari and Hugo Denier van der Gon and Laura Gallardo and Ricardo Mu\~{n}oz and Rodrigo Donoso and Maurico Galleguillos and Mauricio Osses and Sebastian Tolvett}, url = {http://www.sciencedirect.com/science/article/pii/S1352231018304345}, doi = {https://doi.org/10.1016/j.atmosenv.2018.06.043}, issn = {1352-2310}, year = {2018}, date = {2018-01-01}, journal = {Atmospheric Environment}, volume = {190}, pages = {195 -- 208}, abstract = {Santiago (33.5°S, 70.5°W), the capital of Chile, is frequently affected by extreme air pollution events during wintertime deteriorating air quality (AQ) and thus affecting the health of its population. Intense residential heating and on-road transport emissions combined with poor circulation and vertical mixing are the main factors responsible for these events. A modelling system composed of a chemistry-transport model (CHIMERE) and a meteorological model (WRF) was implemented to assess the AQ impacts of residential and transportation sources in the Santiago basin. A two-week period of July 2015 with various days with poor AQ was simulated focusing on the impact on AQ with respect to fully inhalable particles (PM2.5) and nitrogen oxides (NOX). Three emission scenarios, within the range of targeted reductions of the decontamination plan of Santiago, were tested; namely 50% reduction of residential emission, 50% reduction of transport emissions and the combination of both. An additional scenario decreasing transport emissions in 10% was carried out to examine whether a linear dependence of surface concentrations on changes in emissions exists. The system was validated against surface and vertically resolved meteorological measurements. The model reproduces the daily surface concentration variability from the AQ monitoring network of Santiago. However, the model not fully captures the emissions variations inferred from the observations which may be due to missing sources such as resuspension of dust. Results show that, during the period studied, although both residential and transportation sources contribute to observed AQ levels in Santiago, reducing transport emissions is more effective in terms of reducing the number of days with pollution events than decreasing residential combustion. This difference in impact is largely due to the spatial distribution of the emission sources. While most of the residential combustion is emitted in the outskirts of the city, most of the transport emissions occur within the city, where most of the stations from AQ monitoring network of Santiago are located. As can be expected, the largest improvement of AQ in Santiago is achieved by the combined reduction of emissions in both sectors. Sensitivity analysis with 10% reduction in transport emissions reveals a linear behavior between emissions and concentrations for NOX and approximate linear behavior for PM2.5. The absence of secondary aerosols formation and dust resuspension in the current simulation could explain this deviation from linearity for fine particles. Nevertheless, it suggests that the results can be used for mitigation policies with emissions reductions below the 50% used in this study.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Santiago (33.5°S, 70.5°W), the capital of Chile, is frequently affected by extreme air pollution events during wintertime deteriorating air quality (AQ) and thus affecting the health of its population. Intense residential heating and on-road transport emissions combined with poor circulation and vertical mixing are the main factors responsible for these events. A modelling system composed of a chemistry-transport model (CHIMERE) and a meteorological model (WRF) was implemented to assess the AQ impacts of residential and transportation sources in the Santiago basin. A two-week period of July 2015 with various days with poor AQ was simulated focusing on the impact on AQ with respect to fully inhalable particles (PM2.5) and nitrogen oxides (NOX). Three emission scenarios, within the range of targeted reductions of the decontamination plan of Santiago, were tested; namely 50% reduction of residential emission, 50% reduction of transport emissions and the combination of both. An additional scenario decreasing transport emissions in 10% was carried out to examine whether a linear dependence of surface concentrations on changes in emissions exists. The system was validated against surface and vertically resolved meteorological measurements. The model reproduces the daily surface concentration variability from the AQ monitoring network of Santiago. However, the model not fully captures the emissions variations inferred from the observations which may be due to missing sources such as resuspension of dust. Results show that, during the period studied, although both residential and transportation sources contribute to observed AQ levels in Santiago, reducing transport emissions is more effective in terms of reducing the number of days with pollution events than decreasing residential combustion. This difference in impact is largely due to the spatial distribution of the emission sources. While most of the residential combustion is emitted in the outskirts of the city, most of the transport emissions occur within the city, where most of the stations from AQ monitoring network of Santiago are located. As can be expected, the largest improvement of AQ in Santiago is achieved by the combined reduction of emissions in both sectors. Sensitivity analysis with 10% reduction in transport emissions reveals a linear behavior between emissions and concentrations for NOX and approximate linear behavior for PM2.5. The absence of secondary aerosols formation and dust resuspension in the current simulation could explain this deviation from linearity for fine particles. Nevertheless, it suggests that the results can be used for mitigation policies with emissions reductions below the 50% used in this study. |
Jayakumar, Kumarasamy; Camarada, María Belén; Dharuman, Venkataraman; Rajesh, Rajendiran; Venkatesan, Rengarajan; Ju, Huangxian; Maniraj, Mahalingam; Rai, Abhishek; Barman, Sudipta Roy; wen, Yangping ACS Applied Materials & Interfaces, 10 (25), pp. 21541–21555, 2018. @article{jayakumar_layer-by-layer-assembled_2018, title = {Layer-by-Layer-Assembled AuNPs-Decorated First-Generation Poly(amidoamine) Dendrimer with Reduced Graphene Oxide Core as Highly Sensitive Biosensing Platform with Controllable 3D Nanoarchitecture for Rapid Voltammetric Analysis of Ultratrace DNA Hybridization}, author = {Kumarasamy Jayakumar and Mar\'{i}a Bel\'{e}n Camarada and Venkataraman Dharuman and Rajendiran Rajesh and Rengarajan Venkatesan and Huangxian Ju and Mahalingam Maniraj and Abhishek Rai and Sudipta Roy Barman and Yangping wen}, url = {https://doi.org/10.1021/acsami.8b03236}, doi = {10.1021/acsami.8b03236}, year = {2018}, date = {2018-01-01}, journal = {ACS Applied Materials & Interfaces}, volume = {10}, number = {25}, pages = {21541--21555}, abstract = {The structure and electrochemical properties of layer-by-layer-assembled gold nanoparticles (AuNPs)-decorated first-generation (G1) poly(amidoamine) dendrimer (PD) with reduced graphene oxide (rGO) core as a highly sensitive and label-free biosensing platform with a controllable three-dimensional (3D) nanoarchitecture for the rapid voltammetric analysis of DNA hybridization at ultratrace levels were characterized. Mercaptopropinoic acid (MPA) was self-assembled onto Au substrate, then GG1PD formed by the covalent functionalization between the amino terminals of G1PD and carboxyl terminals of rGO was covalently linked onto MPA, and finally AuNPs were decorated onto GG1PD by strong physicochemical interaction between AuNPs and −OH of rGO in GG1PD, which was characterized through different techniques and confirmed by computational calculation. This 3D controllable thin-film electrode was optimized and evaluated using [Fe(CN)6]3\textendash/4\textendash as the redox probe and employed to covalently immobilize thiol-functionalized single-stranded DNA as biorecognition element to form the DNA nanobiosensor, which achieved fast, ultrasensitive, and high-selective differential pulse voltammetric analysis of DNA hybridization in a linear range from 1 × 10\textendash6 to 1 × 10\textendash13 g m\textendash1 with a low detection limit of 9.07 × 10\textendash14 g m\textendash1. This work will open a new pathway for the controllable 3D nanoarchitecture of the layer-by-layer-assembled metal nanoparticles-functionalized lower-generation PD with two-dimensional layered nanomaterials as cores that can be employed as ultrasensitive and label-free nanobiodevices for the fast diagnosis of specific genome diseases in the field of biomedicine.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The structure and electrochemical properties of layer-by-layer-assembled gold nanoparticles (AuNPs)-decorated first-generation (G1) poly(amidoamine) dendrimer (PD) with reduced graphene oxide (rGO) core as a highly sensitive and label-free biosensing platform with a controllable three-dimensional (3D) nanoarchitecture for the rapid voltammetric analysis of DNA hybridization at ultratrace levels were characterized. Mercaptopropinoic acid (MPA) was self-assembled onto Au substrate, then GG1PD formed by the covalent functionalization between the amino terminals of G1PD and carboxyl terminals of rGO was covalently linked onto MPA, and finally AuNPs were decorated onto GG1PD by strong physicochemical interaction between AuNPs and −OH of rGO in GG1PD, which was characterized through different techniques and confirmed by computational calculation. This 3D controllable thin-film electrode was optimized and evaluated using [Fe(CN)6]3–/4– as the redox probe and employed to covalently immobilize thiol-functionalized single-stranded DNA as biorecognition element to form the DNA nanobiosensor, which achieved fast, ultrasensitive, and high-selective differential pulse voltammetric analysis of DNA hybridization in a linear range from 1 × 10–6 to 1 × 10–13 g m–1 with a low detection limit of 9.07 × 10–14 g m–1. This work will open a new pathway for the controllable 3D nanoarchitecture of the layer-by-layer-assembled metal nanoparticles-functionalized lower-generation PD with two-dimensional layered nanomaterials as cores that can be employed as ultrasensitive and label-free nanobiodevices for the fast diagnosis of specific genome diseases in the field of biomedicine. |
Huijse, Pablo; Estévez, Pablo A; Förster, Francisco; Daniel, Scott F; Connolly, Andrew J; Protopapas, Pavlos; Carrasco, Rodrigo; Príncipe, José C Robust Period Estimation Using Mutual Information for Multiband Light Curves in the Synoptic Survey Era Journal Article The Astrophysical Journal Supplement Series, 236 (1), pp. 12, 2018. @article{0067-0049-236-1-12, title = {Robust Period Estimation Using Mutual Information for Multiband Light Curves in the Synoptic Survey Era}, author = {Pablo Huijse and Pablo A Est\'{e}vez and Francisco F\"{o}rster and Scott F Daniel and Andrew J Connolly and Pavlos Protopapas and Rodrigo Carrasco and Jos\'{e} C Pr\'{i}ncipe}, url = {http://stacks.iop.org/0067-0049/236/i=1/a=12}, year = {2018}, date = {2018-01-01}, journal = {The Astrophysical Journal Supplement Series}, volume = {236}, number = {1}, pages = {12}, abstract = {The Large Synoptic Survey Telescope (LSST) will produce an unprecedented amount of light curves using six optical bands. Robust and efficient methods that can aggregate data from multidimensional sparsely sampled time-series are needed. In this paper we present a new method for light curve period estimation based on quadratic mutual information (QMI). The proposed method does not assume a particular model for the light curve nor its underlying probability density and it is robust to non-Gaussian noise and outliers. By combining the QMI from several bands the true period can be estimated even when no single-band QMI yields the period. Period recovery performance as a function of average magnitude and sample size is measured using 30,000 synthetic multiband light curves of RR Lyrae and Cepheid variables generated by the LSST Operations and Catalog simulators. The results show that aggregating information from several bands is highly beneficial in LSST sparsely sampled time-series, obtaining an absolute increase in period recovery rate up to 50%. We also show that the QMI is more robust to noise and light curve length (sample size) than the multiband generalizations of the Lomb\textendashScargle and AoV periodograms, recovering the true period in 10%\textendash30% more cases than its competitors. A python package containing efficient Cython implementations of the QMI and other methods is provided.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Large Synoptic Survey Telescope (LSST) will produce an unprecedented amount of light curves using six optical bands. Robust and efficient methods that can aggregate data from multidimensional sparsely sampled time-series are needed. In this paper we present a new method for light curve period estimation based on quadratic mutual information (QMI). The proposed method does not assume a particular model for the light curve nor its underlying probability density and it is robust to non-Gaussian noise and outliers. By combining the QMI from several bands the true period can be estimated even when no single-band QMI yields the period. Period recovery performance as a function of average magnitude and sample size is measured using 30,000 synthetic multiband light curves of RR Lyrae and Cepheid variables generated by the LSST Operations and Catalog simulators. The results show that aggregating information from several bands is highly beneficial in LSST sparsely sampled time-series, obtaining an absolute increase in period recovery rate up to 50%. We also show that the QMI is more robust to noise and light curve length (sample size) than the multiband generalizations of the Lomb–Scargle and AoV periodograms, recovering the true period in 10%–30% more cases than its competitors. A python package containing efficient Cython implementations of the QMI and other methods is provided. |
Melo, Juan P; Ríos, Paulina L; Povea, Paula; Morales-Verdejo, Cesar; Camarada, María B ACS Omega, 3 (7), pp. 7278-7287, 2018. @article{doi:10.1021/acsomega.8b00837, title = {Graphene Oxide Quantum Dots as the Support for the Synthesis of Gold Nanoparticles and Their Applications as New Catalysts for the Decomposition of Composite Solid Propellants}, author = {Juan P Melo and Paulina L R\'{i}os and Paula Povea and Cesar Morales-Verdejo and Mar\'{i}a B Camarada}, url = {https://doi.org/10.1021/acsomega.8b00837}, doi = {10.1021/acsomega.8b00837}, year = {2018}, date = {2018-01-01}, journal = {ACS Omega}, volume = {3}, number = {7}, pages = {7278-7287}, abstract = {Graphene oxide quantum dot (GOQD) and reduced GOOD (rGOQD) were synthetized using a simple and straight methodology based on an oxidative treatment and sonication. GOQD and rGOQD were used as supporting agents for the in situ generation of gold nanoparticles, avoiding the use of additional stabilizers. GOQD resulted as a better support than rGOQD because of the presence of higher functional groups that can interact with gold. Theoretical studies through density functional theory revealed the important role of the epoxy groups of GOQD on the stabilization of gold. GOQD and GOQD-Au were tested for the first time as catalysts for the decomposition of solid composite propellants. GOQD not only lowered the decomposition temperature of ammonium perchlorate (AP) but also enhanced the exothermic heat of AP, in comparison to graphene and GO. GOQD-Au increased the energy release; however, the effect on the decrease of the decomposition temperature of AP was not as significant as other previous reported catalysts.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Graphene oxide quantum dot (GOQD) and reduced GOOD (rGOQD) were synthetized using a simple and straight methodology based on an oxidative treatment and sonication. GOQD and rGOQD were used as supporting agents for the in situ generation of gold nanoparticles, avoiding the use of additional stabilizers. GOQD resulted as a better support than rGOQD because of the presence of higher functional groups that can interact with gold. Theoretical studies through density functional theory revealed the important role of the epoxy groups of GOQD on the stabilization of gold. GOQD and GOQD-Au were tested for the first time as catalysts for the decomposition of solid composite propellants. GOQD not only lowered the decomposition temperature of ammonium perchlorate (AP) but also enhanced the exothermic heat of AP, in comparison to graphene and GO. GOQD-Au increased the energy release; however, the effect on the decrease of the decomposition temperature of AP was not as significant as other previous reported catalysts. |
Peredo, Oscar; Baeza, Daniel; á, Juli; é, Jos A path-level exact parallelization strategy for sequential simulation Journal Article Computers & Geosciences, 110 , pp. 10–22, 2018. @article{DBLP:journals/gandc/PeredoBOH18, title = {A path-level exact parallelization strategy for sequential simulation}, author = {Oscar Peredo and Daniel Baeza and Juli \'{a} and Jos \'{e}}, url = {https://doi.org/10.1016/j.cageo.2017.09.011}, doi = {10.1016/j.cageo.2017.09.011}, year = {2018}, date = {2018-01-01}, journal = {Computers & Geosciences}, volume = {110}, pages = {10--22}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Camarada, M B; Comer, J; Poblete, H; Singam, Azhagiya E R; Marquez-Miranda, V; Morales-Verdejo, C; Gonzalez-Nilo, F D Experimental and Computational Characterization of the Interaction between Gold Nanoparticles and Polyamidoamine Dendrimers Journal Article Langmuir, 34 (34), pp. 10063-10072, 2018, (PMID: 30074805). @article{doi:10.1021/acs.langmuir.8b01809, title = {Experimental and Computational Characterization of the Interaction between Gold Nanoparticles and Polyamidoamine Dendrimers}, author = {M B Camarada and J Comer and H Poblete and E R Azhagiya Singam and V Marquez-Miranda and C Morales-Verdejo and F D Gonzalez-Nilo}, url = {https://doi.org/10.1021/acs.langmuir.8b01809}, doi = {10.1021/acs.langmuir.8b01809}, year = {2018}, date = {2018-01-01}, journal = {Langmuir}, volume = {34}, number = {34}, pages = {10063-10072}, abstract = {Dendrimers provide a means to control the synthesis of gold nanoparticles and stabilize their suspensions. However, design of improved dendrimers for this application is hindered by a lack of understanding how the dendrimers and synthesis conditions determine nanoparticle morphology and suspension stability. In the present work, we evaluate the effect of polyamidoamine (PAMAM) dendrimers terminated with different functional groups (−OH or −NH3+) and different synthesis conditions on the morphology of the resulting gold nanoparticles and their stability in solution. We leverage molecular dynamics (MD) simulations to identify the atomic interactions that underlie adsorption of PAMAM dendrimers to gold surface and how the thermodynamics of this adsorption depends on the terminal functional groups of the dendrimers. We find that gold nanoparticles formed with hydroxyl-terminated PAMAM (PAMAM\textendashOH) rapidly aggregate, whereas those formed with PAMAM\textendashNH3+ are stable in solution for months of storage. Synthesis under ultrasound sonication is shown to be more rapid than that under agitation, with sonication producing smaller nanoparticles. Free-energy calculations in MD simulations show that all dendrimers have a high affinity for the gold surface, although PAMAM\textendashOH and its oxidized aldehyde form (PAMAM\textendashCHO) have a greater affinity for the nanoparticle surface than PAMAM\textendashNH3+. Although adsorption of PAMAM\textendashOH and PAMAM\textendashCHO has both favorable entropy and enthalpy, adsorption of PAMAM\textendashNH3+ is driven by a strong enthalpic component subject to an unfavorable entropic component.}, note = {PMID: 30074805}, keywords = {}, pubstate = {published}, tppubtype = {article} } Dendrimers provide a means to control the synthesis of gold nanoparticles and stabilize their suspensions. However, design of improved dendrimers for this application is hindered by a lack of understanding how the dendrimers and synthesis conditions determine nanoparticle morphology and suspension stability. In the present work, we evaluate the effect of polyamidoamine (PAMAM) dendrimers terminated with different functional groups (−OH or −NH3+) and different synthesis conditions on the morphology of the resulting gold nanoparticles and their stability in solution. We leverage molecular dynamics (MD) simulations to identify the atomic interactions that underlie adsorption of PAMAM dendrimers to gold surface and how the thermodynamics of this adsorption depends on the terminal functional groups of the dendrimers. We find that gold nanoparticles formed with hydroxyl-terminated PAMAM (PAMAM–OH) rapidly aggregate, whereas those formed with PAMAM–NH3+ are stable in solution for months of storage. Synthesis under ultrasound sonication is shown to be more rapid than that under agitation, with sonication producing smaller nanoparticles. Free-energy calculations in MD simulations show that all dendrimers have a high affinity for the gold surface, although PAMAM–OH and its oxidized aldehyde form (PAMAM–CHO) have a greater affinity for the nanoparticle surface than PAMAM–NH3+. Although adsorption of PAMAM–OH and PAMAM–CHO has both favorable entropy and enthalpy, adsorption of PAMAM–NH3+ is driven by a strong enthalpic component subject to an unfavorable entropic component. |
Riaz, R; Vanaverbeke, S; Schleicher, D R G Formation of multiple low-mass stars, brown dwarfs, and planemos via gravitational collapse Journal Article Monthly Notices of the Royal Astronomical Society, 478 (4), pp. 5460-5472, 2018. @article{doi:10.1093/mnras/sty1409, title = {Formation of multiple low-mass stars, brown dwarfs, and planemos via gravitational collapse}, author = {R Riaz and S Vanaverbeke and D R G Schleicher}, url = {http://dx.doi.org/10.1093/mnras/sty1409}, doi = {10.1093/mnras/sty1409}, year = {2018}, date = {2018-01-01}, journal = {Monthly Notices of the Royal Astronomical Society}, volume = {478}, number = {4}, pages = {5460-5472}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Pereira, Jordi; Ritt, Marcus; Vásquez, Óscar C A memetic algorithm for the cost-oriented robotic assembly line balancing problem Journal Article Computers & Operations Research, 99 , pp. 249 - 261, 2018, ISSN: 0305-0548. @article{PEREIRA2018249, title = {A memetic algorithm for the cost-oriented robotic assembly line balancing problem}, author = {Jordi Pereira and Marcus Ritt and \'{O}scar C V\'{a}squez}, url = {http://www.sciencedirect.com/science/article/pii/S0305054818301850}, doi = {https://doi.org/10.1016/j.cor.2018.07.001}, issn = {0305-0548}, year = {2018}, date = {2018-01-01}, journal = {Computers & Operations Research}, volume = {99}, pages = {249 - 261}, abstract = {In order to minimize costs, manufacturing companies have been relying on assembly lines for the mass production of commodity goods. Among other issues, the successful operation of an assembly line requires balancing work among the stations of the line in order to maximize its efficiency, a problem known in the literature as the assembly line balancing problem, ALBP. In this work, we consider an ALBP in which task assignment and equipment decisions are jointly considered, a problem that has been denoted as the robotic ALBP. Moreover, we focus on the case in which equipment has different costs, leading to a cost-oriented formulation. In order to solve the problem, which we denote as the cost-oriented robotic assembly line balancing problem, cRALBP, a hybrid metaheuristic is proposed. The metaheuristic embeds results obtained for two special cases of the problem within a genetic algorithm in order to obtain a memetic algorithm, applicable to the general problem. An extensive computational experiment shows the advantages of the hybrid approach and how each of the components of the algorithm contributes to the overall ability of the method to obtain good solutions.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In order to minimize costs, manufacturing companies have been relying on assembly lines for the mass production of commodity goods. Among other issues, the successful operation of an assembly line requires balancing work among the stations of the line in order to maximize its efficiency, a problem known in the literature as the assembly line balancing problem, ALBP. In this work, we consider an ALBP in which task assignment and equipment decisions are jointly considered, a problem that has been denoted as the robotic ALBP. Moreover, we focus on the case in which equipment has different costs, leading to a cost-oriented formulation. In order to solve the problem, which we denote as the cost-oriented robotic assembly line balancing problem, cRALBP, a hybrid metaheuristic is proposed. The metaheuristic embeds results obtained for two special cases of the problem within a genetic algorithm in order to obtain a memetic algorithm, applicable to the general problem. An extensive computational experiment shows the advantages of the hybrid approach and how each of the components of the algorithm contributes to the overall ability of the method to obtain good solutions. |
Ortega, Daniela E; Cortés-Arriagada, Diego; Toro-Labbé, Alejandro Mechanistic details of ethylene polymerization reaction using methallyl nickel(ii) catalysts Journal Article Phys. Chem. Chem. Phys., pp. -, 2018. @article{C8CP03955K, title = {Mechanistic details of ethylene polymerization reaction using methallyl nickel(ii) catalysts}, author = {Daniela E Ortega and Diego Cort\'{e}s-Arriagada and Alejandro Toro-Labb\'{e}}, url = {http://dx.doi.org/10.1039/C8CP03955K}, doi = {10.1039/C8CP03955K}, year = {2018}, date = {2018-01-01}, journal = {Phys. Chem. Chem. Phys.}, pages = {-}, publisher = {The Royal Society of Chemistry}, abstract = {The mechanism of ethylene polymerization by means of neutral methallyl-Ni(ii) complexes has been studied by quantum chemical calculations. Two isomer complexes having different ligand functionalization at the ortho or para position, and co-activated with trispentafluorephenylborane [B(C6F5)3], were studied according to the Cossee\textendashArlman's mechanism. Comparison of the reaction mechanism of both isomers shows that energy barriers strongly depend on ligand-functionalization and are mostly due to structural rearrangements. In addition, it was found that para-functionalization can be distinguished by favorable σ-donation whereas ortho-functionalization is more prone to a π back-donation process. Our results concerning the polymerization process for ortho and para isomers not only provide a theoretical perspective of available experimental data, but also explain the experimentally observed higher molecular weight of the methallyl-Ni(ii) ortho isomer co-catalyzed by B(C6F5)3, revealing the role of ligand-functionalization in polyethylene productio}, keywords = {}, pubstate = {published}, tppubtype = {article} } The mechanism of ethylene polymerization by means of neutral methallyl-Ni(ii) complexes has been studied by quantum chemical calculations. Two isomer complexes having different ligand functionalization at the ortho or para position, and co-activated with trispentafluorephenylborane [B(C6F5)3], were studied according to the Cossee–Arlman's mechanism. Comparison of the reaction mechanism of both isomers shows that energy barriers strongly depend on ligand-functionalization and are mostly due to structural rearrangements. In addition, it was found that para-functionalization can be distinguished by favorable σ-donation whereas ortho-functionalization is more prone to a π back-donation process. Our results concerning the polymerization process for ortho and para isomers not only provide a theoretical perspective of available experimental data, but also explain the experimentally observed higher molecular weight of the methallyl-Ni(ii) ortho isomer co-catalyzed by B(C6F5)3, revealing the role of ligand-functionalization in polyethylene productio |
Alvarado, D; Moreira, A; Moreno, R; Strbac, G Transmission Network Investment with Distributed Energy Resources and Distributionally Robust Security Journal Article IEEE Transactions on Power Systems, pp. 1-1, 2018, ISSN: 0885-8950. @article{8447238, title = {Transmission Network Investment with Distributed Energy Resources and Distributionally Robust Security}, author = {D Alvarado and A Moreira and R Moreno and G Strbac}, doi = {10.1109/TPWRS.2018.2867226}, issn = {0885-8950}, year = {2018}, date = {2018-01-01}, journal = {IEEE Transactions on Power Systems}, pages = {1-1}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Rodríguez, M; Magna-Verdugo, Carolina; Abell, José Influence of Soil-Structure-Interaction in Shear-wall RC Buildings Fragility Curves 2018. @unknown{unknown, title = {Influence of Soil-Structure-Interaction in Shear-wall RC Buildings Fragility Curves}, author = {M Rodr\'{i}guez and Carolina Magna-Verdugo and Jos\'{e} Abell}, year = {2018}, date = {2018-01-01}, keywords = {}, pubstate = {published}, tppubtype = {unknown} } |
Jayakumar, Kumarasamy; Camarada, María Belén; Rajesh, Rajendiran; Venkatesan, Rengarajan; Ju, Huangxian; Dharuman, Venkatraman; Wen, Yangping Biosensors and Bioelectronics, 2018, ISSN: 0956-5663. @article{JAYAKUMAR2018, title = {Layer-by-layer assembled gold nanoparticles/lower-generation (Gn≤3) polyamidoamine dendrimers-grafted reduced graphene oxide nanohybrids with 3D fractal architecture for fast, ultra-trace, and label-free electrochemical gene nanobiosensors}, author = {Kumarasamy Jayakumar and Mar\'{i}a Bel\'{e}n Camarada and Rajendiran Rajesh and Rengarajan Venkatesan and Huangxian Ju and Venkatraman Dharuman and Yangping Wen}, url = {http://www.sciencedirect.com/science/article/pii/S0956566318306249}, doi = {https://doi.org/10.1016/j.bios.2018.08.032}, issn = {0956-5663}, year = {2018}, date = {2018-01-01}, journal = {Biosensors and Bioelectronics}, abstract = {Three layer-by-layer (LBL) assembled gold nanoparticles (AuNPs)/lower-generation (Gn≤3) polyamidoamine dendrimer (PD) with reduced graphene oxide (rGO) as the core/mercaptopropinoic acid (MPA)/Au were successfully fabricated and employed as electrochemical gene nanobiosensing platforms with three-dimensional (3D) fractal nanoarchitecture for fast, ultra-trace determination of label-free DNA hybridization. Three Gn≤3PD were initially grafted to graphite oxide (GO) via the covalent functionalization between amino terminals of PD and carboxyl terminals of GO where a concomitant reduction of GO, which were covalently linked onto MPA that was self-assembled onto Au substrate, and finally AuNPs were encapsulated onto GG1PD by strong physicochemical interaction between AuNPs and -OH of rGO in GG1PD, Their morphologies, structures, electrochemical properties, and gene nanobiosensing performances were characterized and evaluated. AuNPs/GG2PD-based probe displayed the best excellent structural stability, lowest mobility on solid surface with the increasing charge resistance, widest linear range (1.1 × 10-6 \textendash 1 × 10-18), and the lowest limit of detection (1.87 × 10-19 M) in comparison with both AuNPs/GG1PD-based and AuNPs/GG3PD-based probes. This work will provide a new candidate for the development of metal nanoparticles functionalized PD with inorganic nonmetallic nanomaterials as cores with 3D fractal nanoarchitecture and promising electrochemical gene nanobiosensing platforms based on dendrimer-nanoinorganic hybrids with 3D nanoarchitectures and LBL assembly for fast and ultra-trace detection of label-free DNA hybridization with potential application in bioanalysis and medical diagnosis of genetic diseases.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Three layer-by-layer (LBL) assembled gold nanoparticles (AuNPs)/lower-generation (Gn≤3) polyamidoamine dendrimer (PD) with reduced graphene oxide (rGO) as the core/mercaptopropinoic acid (MPA)/Au were successfully fabricated and employed as electrochemical gene nanobiosensing platforms with three-dimensional (3D) fractal nanoarchitecture for fast, ultra-trace determination of label-free DNA hybridization. Three Gn≤3PD were initially grafted to graphite oxide (GO) via the covalent functionalization between amino terminals of PD and carboxyl terminals of GO where a concomitant reduction of GO, which were covalently linked onto MPA that was self-assembled onto Au substrate, and finally AuNPs were encapsulated onto GG1PD by strong physicochemical interaction between AuNPs and -OH of rGO in GG1PD, Their morphologies, structures, electrochemical properties, and gene nanobiosensing performances were characterized and evaluated. AuNPs/GG2PD-based probe displayed the best excellent structural stability, lowest mobility on solid surface with the increasing charge resistance, widest linear range (1.1 × 10-6 – 1 × 10-18), and the lowest limit of detection (1.87 × 10-19 M) in comparison with both AuNPs/GG1PD-based and AuNPs/GG3PD-based probes. This work will provide a new candidate for the development of metal nanoparticles functionalized PD with inorganic nonmetallic nanomaterials as cores with 3D fractal nanoarchitecture and promising electrochemical gene nanobiosensing platforms based on dendrimer-nanoinorganic hybrids with 3D nanoarchitectures and LBL assembly for fast and ultra-trace detection of label-free DNA hybridization with potential application in bioanalysis and medical diagnosis of genetic diseases. |
Candlish, G N; Smith, R; Jaffé, Y; Cortesi, A Consequences of the external field effect for MOND disc galaxies in galaxy clusters Journal Article Monthly Notices of the Royal Astronomical Society, 480 (4), pp. 5362-5379, 2018. @article{doi:10.1093/mnras/sty2228, title = {Consequences of the external field effect for MOND disc galaxies in galaxy clusters}, author = {G N Candlish and R Smith and Y Jaff\'{e} and A Cortesi}, url = {http://dx.doi.org/10.1093/mnras/sty2228}, doi = {10.1093/mnras/sty2228}, year = {2018}, date = {2018-01-01}, journal = {Monthly Notices of the Royal Astronomical Society}, volume = {480}, number = {4}, pages = {5362-5379}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Muñoz, Michelle; Siegmund, Daniel; Gomez, Alejandra; Godoy, Fernando; Fierro, Angelica; Llanos, Leonel; Aravena, Daniel; Metzler-Nolte, Nils Dalton Trans., pp. –, 2018. @article{munoz_influence_2018, title = {Influence of the substituent on the phosphine ligand in novel rhenium (I) aldehydes. Synthesis, computational studies and first insights into antiproliferative activity.}, author = {Michelle Mu\~{n}oz and Daniel Siegmund and Alejandra Gomez and Fernando Godoy and Angelica Fierro and Leonel Llanos and Daniel Aravena and Nils Metzler-Nolte}, url = {http://dx.doi.org/10.1039/C8DT03160F}, doi = {10.1039/C8DT03160F}, year = {2018}, date = {2018-01-01}, journal = {Dalton Trans.}, pages = {--}, abstract = {Cyrhetrenyl derivatives [(η5-C5H4CHO)Re(CO)2PR3)] R = Me (2a), Ph (2b) and Cy (2c) were synthetized by a photochemical reaction with a starting material [(η5-C5H4CHO)Re(CO)3] (1) using corresponding phosphines. The complexes were fully characterized by FT-IR, 1H, 13C and 31P NMR spectroscopies, elemental analysis and mass spectrometry. The molecular structures of 2a-c have also been determined. The electronic structural calculation and electrochemical studies are in sound agreement with the effect of the substitution of one carbonyl group by a phosphine ligand. Additionally, the complexes 2a-c, as well as 1, were studied on the human cancer cell lines HT-29 and PT-45 by an MTT assay. The triphenylphosphine derivative 2b exhibited pronounced cytotoxic effects on both cell lines and it is ca. 1.5 times more potent than cisplatin.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Cyrhetrenyl derivatives [(η5-C5H4CHO)Re(CO)2PR3)] R = Me (2a), Ph (2b) and Cy (2c) were synthetized by a photochemical reaction with a starting material [(η5-C5H4CHO)Re(CO)3] (1) using corresponding phosphines. The complexes were fully characterized by FT-IR, 1H, 13C and 31P NMR spectroscopies, elemental analysis and mass spectrometry. The molecular structures of 2a-c have also been determined. The electronic structural calculation and electrochemical studies are in sound agreement with the effect of the substitution of one carbonyl group by a phosphine ligand. Additionally, the complexes 2a-c, as well as 1, were studied on the human cancer cell lines HT-29 and PT-45 by an MTT assay. The triphenylphosphine derivative 2b exhibited pronounced cytotoxic effects on both cell lines and it is ca. 1.5 times more potent than cisplatin. |
Förster, F; Moriya, T J; Maureira, J C; Anderson, J P; Blinnikov, S; Bufano, F; Cabrera-Vives, G; Clocchiatti, A; de Jaeger, T; Estévez, P A; Galbany, L; González-Gaitán, S; Gräfener, G; Hamuy, M; Hsiao, E Y; Huentelemu, P; Huijse, P; Kuncarayakti, H; Martínez, J; Medina, G; E., Olivares F; Pignata, G; Razza, A; Reyes, I; Martín, San J; Smith, R C; Vera, E; Vivas, A K; de Postigo, Ugarte A; Yoon, S -C; Ashall, C; Fraser, M; Gal-Yam, A; Kankare, E; Guillou, Le L; Mazzali, P A; Walton, N A; Young, D R The delay of shock breakout due to circumstellar material evident in most type II supernovae Journal Article Nature Astronomy, 2018, ISSN: 2397-3366. @article{forster_delay_2018, title = {The delay of shock breakout due to circumstellar material evident in most type II supernovae}, author = {F F\"{o}rster and T J Moriya and J C Maureira and J P Anderson and S Blinnikov and F Bufano and G Cabrera-Vives and A Clocchiatti and T de Jaeger and P A Est\'{e}vez and L Galbany and S Gonz\'{a}lez-Gait\'{a}n and G Gr\"{a}fener and M Hamuy and E Y Hsiao and P Huentelemu and P Huijse and H Kuncarayakti and J Mart\'{i}nez and G Medina and F Olivares E. and G Pignata and A Razza and I Reyes and J San Mart\'{i}n and R C Smith and E Vera and A K Vivas and A de Ugarte Postigo and S -C Yoon and C Ashall and M Fraser and A Gal-Yam and E Kankare and L Le Guillou and P A Mazzali and N A Walton and D R Young}, url = {https://doi.org/10.1038/s41550-018-0563-4}, doi = {10.1038/s41550-018-0563-4}, issn = {2397-3366}, year = {2018}, date = {2018-01-01}, journal = {Nature Astronomy}, abstract = {Type II supernovae (SNe II) originate from the explosion of hydrogen-rich supergiant massive stars. Their first electromagnetic signature is the shock breakout (SBO), a short-lived phenomenon that can last for hours to days depending on the density at shock emergence. We present 26 rising optical light curves of SN II candidates discovered shortly after explosion by the High Cadence Transient Survey and derive physical parameters based on hydrodynamical models using a Bayesian approach. We observe a steep rise of a few days in 24 out of 26 SN II candidates, indicating the systematic detection of SBOs in a dense circumstellar matter consistent with a mass loss rate of $$textbackslashbackslashdot M$$M textgreater 10-4M[?] yr-1 or a dense atmosphere. This implies that the characteristic hour-timescale signature of stellar envelope SBOs may be rare in nature and could be delayed into longer-lived circumstellar material SBOs in most SNe II.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Type II supernovae (SNe II) originate from the explosion of hydrogen-rich supergiant massive stars. Their first electromagnetic signature is the shock breakout (SBO), a short-lived phenomenon that can last for hours to days depending on the density at shock emergence. We present 26 rising optical light curves of SN II candidates discovered shortly after explosion by the High Cadence Transient Survey and derive physical parameters based on hydrodynamical models using a Bayesian approach. We observe a steep rise of a few days in 24 out of 26 SN II candidates, indicating the systematic detection of SBOs in a dense circumstellar matter consistent with a mass loss rate of $$textbackslashbackslashdot M$$M textgreater 10-4M[?] yr-1 or a dense atmosphere. This implies that the characteristic hour-timescale signature of stellar envelope SBOs may be rare in nature and could be delayed into longer-lived circumstellar material SBOs in most SNe II. |
Meerhoff, Erika; Yannicelli, Beatriz; Dewitte, Boris; Díaz-Cabrera, Ernesto; Retter, Caren Vega; Ramos, Marcel; Bravo, Luis; Concha, Emilio; Vaca, Freddy Hernández; Véliz, David Asymmetric connectivity of the lobster Panulirus pascuensis in remote islands of the southern Pacific: importance for its management and conservation Journal Article Bulletin of Marine Science, 2018. @article{meerhoff_asymmetric_2018, title = {Asymmetric connectivity of the lobster Panulirus pascuensis in remote islands of the southern Pacific: importance for its management and conservation}, author = {Erika Meerhoff and Beatriz Yannicelli and Boris Dewitte and Ernesto D\'{i}az-Cabrera and Caren Vega Retter and Marcel Ramos and Luis Bravo and Emilio Concha and Freddy Hern\'{a}ndez Vaca and David V\'{e}liz}, year = {2018}, date = {2018-01-01}, journal = {Bulletin of Marine Science}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Schmidt, I; Siddikov, M; Musakhanov, M Charmonia suppression in heavy ion collisions: Hot versus cold matter effects Journal Article Phys. Rev. C, 98 (2), pp. 025207, 2018. @article{schmidt_charmonia_2018, title = {Charmonia suppression in heavy ion collisions: Hot versus cold matter effects}, author = {I Schmidt and M Siddikov and M Musakhanov}, url = {https://link.aps.org/doi/10.1103/PhysRevC.98.025207}, doi = {10.1103/PhysRevC.98.025207}, year = {2018}, date = {2018-01-01}, journal = {Phys. Rev. C}, volume = {98}, number = {2}, pages = {025207}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
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