Publicaciones

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

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

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

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

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

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

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

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