Adi-24 Project Director Signature

RESEARCH TEAM GRANTS IN SCIENCE AND TECHNOLOGY 2006 FINAL REPORT

I. PROJECT PRESENTATION

PROJECT TITLE CODE Computer Simulation Laboratory of Nanomaterials and Biological Systems of Experimental Interest ADI-24 PROJECT DIRECTOR SIGNATURE

Gonzalo Gutiérrez Gallardo

CONTACT INFORMATION Las Palmeras 3425, Ñuñoa; Región Metropolitana - MAIN INSTITUTION

Universidad de Chile PERIOD INFORMED April-07 - April 2011

a) Main researchers’ information

MAIN RESEARCHER (Complete Name) SIGNATURE Eduardo Menendez-Proupin

WORKING ADDRESS PHONES EMAIL Dept. Física, Fac. Ciencias, U. [email protected] de Chile

MAIN RESEARCHER (Complete Name) SIGNATURE

Fernando Danilo Gonzalez-Nilo

WORKING ADDRESS PHONES EMAIL

Center for Bioinformatics and Molecular Simulations (CBSM) danilo.gonzaleznilo@gm

Universidad de Talca ail.com 2 Norte 685, Casilla 721, Talca - Chile

b) Associated researchers’ information

ASSOCIATED RESEARCHER (Complete Name) SIGNATURE

Walter Orellana

WORKING ADDRESS PHONES EMAIL Dept. Fisica, UNAB [email protected]

ASSOCIATED RESEARCHER (Complete Name) SIGNATURE

David Laroze

WORKING ADDRESS PHONES EMAIL Instituto de Alta Inv., U. [email protected] Tarapaca

ASSOCIATED RESEARCHER (Complete Name) SIGNATURE

Jaime Henriquez

WORKING ADDRESS PHONES EMAIL Center for Bioinformatics and Molecular Simulations (CBSM)

Universidad de Talca 2 Norte 685, Casilla 721, Talca - Chile

4 II. EXECUTIVE SUMMARY

The Project Anillo ACT-24 is entitled Computer simulation laboratory of Nanomateriales and biological systems of experimental interest, and its main research goal was a) the study of structural, dynamic, mechanic, electronic, magnetic and optical properties of nanomaterials and b) the study of biological systems such as transmembrane proteins (TRP channels) and the catalytic reaction mechanism in enzymes (PEPCK). During the course of the project, new topics arose, such as the interface between an organic material and a metal, shock waves and hypervelocity impacts. These studies were performed by means of computer simulation at the molecular level, which has shown to be a very useful technique in the theoretical study of systems with time and length scale going from the atomic to nanoscopic and, eventually, to microscopic size, such as the systems studied in this proposal. In addition, we explored methodological and technical topics, such as the development of a molecular dynamics code, the installation of a high performance computing system (304 cores) and a database web platform for nanoparticles. The results of these investigations present an interest not only from a basic point of view, but also they are capable of being applied to strategic researchs interest for the development of our country, in areas such as nanotechnology and biotechnology. The Anillo ACT-24 rested on two fundamental pillars: the Group of NanoMaterials, www.gnm.cl, of the Departamento de F´ısica, Facultad de Ciencias of the Universidad de Chile (GNM), and the Center of Bioinformatic and Molecular Simulation,http://cbsm.utalca.cl/, of the Universidad de Talca (CBSM). The synergy generated by this union allowed us to expand the research issues initially pointed out, as well as venture in more applied areas and interactions with the public sector that, in other way, would have been impossible to do. The Anillo begun with a nucleus of three titular researchers, three reasearch associates and a group of collaborators both from Chile and abroad, as well as 10 graduate and undergraduate students. These researchers and students came from Antofagasta, La Serena, Santiago, Talca, Valdivia and Puerto Montt, with collaborators in Brazil, France and Spain, USA, India, Italy, Japan and Sweden. Through the three years of research, our collaborators net grew up, and 4 postdoctoral researchers, 25 graduate and undergraduate students, as well as foreign researchers joined the team. During the course of the project, we worked driving three main areas: scientific research, human resources training and outreach of the research results, to both specialized audience and public at large. The main results obtained by our research are embodied in the 56 (ISI) published papers, as well as more than 100 congress and conference presentations, in addition to other articles published in journals of continental and national circulation. In the issue nano structured materials and bulk properties, we studied the properties of the aluminium oxide in amorphous state and its crystalline phase γ-Al2O3, developing a structural model that presents a good agreement with experiments, which let us quantify the ionic character of the bond, as well as elucidate the change in its vibrational properties as the sample is put under pressure. In the same line, we studied the compound CdTeOx, a material of current importance in the search for greater efficiency in photovoltaic cells: using ab- initio molecular dynamics calculations on this compound in amorphous state, we could correlate the structure to the emission spectra of photoelectrons (XPS) obtained experimentally. Another amorphous material investigated was the CuZr, alloy that forms a metallic glass, which has many applications as structural material due to its excellent mechanical properties. Here we studied, by means of computer simulation, its structure and vibrational states in liquid and amorphous state, determining that the fundamental building block is a distorted icosahedron. The study of the mechanic and elastic properties of materials is an issue that can be addressed with high precision by means of calculations based on quantum mechanics. In this way, we performed a theoretical- experimental work focused on platinum, that allowed us to determine its elastic constants in a wide range of pressures, getting an excellent agreement with the experiments in those ranges where the data is available. Using the same calculation technique, we studied the mechanical properties of the hydroxiapatite and fluorapatite, key components of the enamel and body of the teeth. In particular, the fluorapatite is found in sick teeth, degrading its mechanical strength. Properties of surfaces and interfaces was another research topic, for both semiconductor and metallic systems. Here we performed basic studies, as well as applications to specific material physics problems and biological systems, working the researchers from GNM (U. de Chile) and the CBSM (U. Talca) in close contact. Thus, joining efforts and experiences, we could address problems from a theoretical-experimental point of view, in organic and inorganic systems. Below we highlight the main achievements. In collaboration with researchers from Universidad de Sevilla, we studied the adsorption of gold atoms in anatase nitrogen surfaces, a titanium oxide variant with photocatalytic properties of great current interest in the search for stable and cheap catalyzers that can be activated by light. Another study of surface properties was carried out together with an experimental group from U. de Chile: we studied the influence of edges in the electric conductivity of thin gold films. Also, we determined the potential energy barrier between grain boundaries using quantum mechanics calculations and images of the TEM microscope. In the area of interfaces between organic and metallic systems, we highlight the study about adsorption of the oligopeptide RGD in titanium dioxide. This topic has direct relationship with the response of tissues to titanium implants, vastly used nowadays in medicine, since the titanium oxide is the natural interface between tissues and titanium (see figure). In the field of biology is possible also to identify certain immunological responses through the interactions between atomic gold structures and proteins such as opsonin, fibronectin and others. We modeled such a system with gold clusters interacting with thiols, obtaining that the interaction of the organic compound was energetically more stable in the deprotonated state than in the protoned state. Finally, another study performed is realted to the corrosion of metallic oxides by organic acids, a problem of practical importance both in industry as in laboratory. In particular, we studied copper and zinc oxides attacked by formic acid, finding through quantum mechanics calculations that copper has a much higher resistence, due to the interaction that, unlike zinc, covers an hydroxylated layer and a molecule of water.

(a) Aspartate molecule on TiO2 surface. (b) AGS-FA-PAMAM-QDot in tumoral cell

Figura 1: Example of metal-organic interfaces and QD-dendrimers. The sutdy of quantum dots was an issue raised from the beginning, but was soon extended to its interaction with organic systems. This issue was addressed in different levels of complexity and approximations. One of the studies undertaken is related to the behavior of a quantum dot under a non-constant magnetic field, using the approximation of effective mass. In the same way, we studied the magneto-optic properties of the semiconductor CdxZn1−xSe, showing that the thermal annealing produces evaporation of Cd, modifies the form of quantum confinement and allows to tune in its magnetic properties. The theoretical-experimental study undertaken jointly with the Institute of Chemistry of the U. de Talca, in relation with the synthesis and characterization of the complex dendrimer-quantum dot, is particularly interesting and of great importance due to its application to obtaining images of tumor cells. In fact, such is the progress in this investigation that a first test has become possible in the cell imaging system, distinguishing tumor cells from healthy ones. Carbon Nanotubes (CNT) is another issue initially proposed, in particular its interaction with molecules, and its possible use as sensors. We studied the absorption of NH3, NO2,H2O and O2 over CNT that had a double vacancy, assuming it would act as active site. However, due to a weak van der Waals interaction, our results suggest that such a defective CNT is not a good candidate for a sensor. We also studied CNTs as hydrogen storage materials, a hot topic because of the search for new energy sources; the energy involved in the H2 absortion and desorption process, obtained by means of molecular dynamics, indicate that nanopores produced by irradiation could be successfully used as a hydrogen storage system. Another project explores the covalent and non- covalent mechanism for the attachment iron porphyrins (FeP) on the surface of single-walled CNT. Nanomagnetism, that is, the magnetic properties of nano-materials was an important topic studied in the Anillo. Our contribution in this area ranges from analysis of thermal and dynamics properties of magnetic chain (nanowires), caracterization of ferrofluids, to quantum level studies of the adsorption of magnetic nanoparticles (Fe) on semiconductors surfaces, as well as the influence of the co-linear magnetism to the total energy in iron at high pressure. In the study of biological systems by large-scale computer simulation our Anillo did important contributions. For example, we performed molecular level simulation of K+ channels: potassium channels are undoubtedly one of the most enigmatic and more studied proteins in biophysics. These transmembrane proteins are the clue for electrical signals of our nervous system, as well as being involved in several neurodegenerative diseases. Several studies have found that in some kind of cancer, like gastric cancer, these proteins are over-expressed and probably have an important role in this disease. In the field of therapies pain relief the K+ channels are used as an important target for design of new anesthetics. Results from molecular simulations allowed us to reinterpret the functional importance of two key aminoacids participating in the sensed temperature TRPV1 K+ channel activation. In the same way, computational predictions based in the analysis of long molecular dynamics simulations allowed us to identify the aminoacids involved in the modulation of electrostatic potential, which regulates the pass of ions across the hSlo K+ channels. The study of enzymatic catalysis represent another successful application of computer simulation to proteins. Using a hybrid scheme which include quantum mechanics/molecular mechanics (QM/MM), we performed, together with U. Santiago researchers, a structural study of the transition states of the decarboxylation reaction that takes place in the active site of the PEPCK protein. The results obtained so far have allowed us to analyze in detail the role of two metals that take part of the catalytic reaction of this enzyme, as well as transitory deprotonation processes, that are not feasible to analyze by other means. Computational assisted drug design in also an area where the our experience in the use of different techniques allowed to tackle several problems, mainly associated to protein-ligand interactions. Thus, by means of a hybrid QM/MM method, we studied non-covalent bonds (hydrogen bonds) between ligands and active sites in kinasas proteins which appear in cancer, Alzheimer and other pathologies. For example, one of our results shows the energy of the hydrogen bond is the principal component of the interaction. Following the research-driving idea that some biological problems can be better understood through a molecular level model, we explore the study of systems far from equilibrium. We have collaborated with physicians of Arauco Clinic to study of the effect of shock waves on biological systems. The motivation is the increasing use of shock wave therapy in the treatment of fractures and wounds, and the lack of knowledge about the interaction of shock waves with human tissue. To assist in this regard, preliminary we have simulated at atomic level the effects of shock waves in inorganic systems like an argon block, describing in detail the fracture process that occurs there. At the same time to these efforts, we want to describe at the atomic level the damage produced by the impact of small projectiles on organic and inorganic matter. Promising results in the case of a copper nano projectile against a target allows us to look with optimism the results of this line of research. Interestingly, our activities not only consisted of “papers” research, but also applied scientific work at international level. In this sense, we are proud of two achievements: the creation of the Collaboratory for Structural Nanobiology (http://nanobiology.utalca.cl/), in collaboration to the National Institute of Cancer, USA, which is a web tool to facilitate the interaction of researchers who are working in nanobiology, health and medicine. Also, we created “from scratch.a computer simulation package called Las Palmeras Molecular Dynamics, www.lpmd.cl, which can be used to simulate systems at the atomic level, and to visualize the atoms or molecules; it is freely distributed under the GPL license. Regarding scientific infrastructure, it included the creation of three laboratories: the laboratory of the Group of Nanomaterials (www.gnm.cl) at the U. Chile, the Protein Engineering laboratory and the Electron Microscopy lab, at U. of Talca. Besides these laboratories, we installed the Center of High Performance Computing, funded jointly by our Anillo and U. Talca, which has a total of 308 cores interconnected with an InfiniBand network, ideal to run parallel software, and where we have performed most of the large-scale simulations. We have also installed a smaller cluster at the University of Chile. The design, setup and running of these facilities has been a major effort from the standpoint of technical and administrative work, which has given us vast experience of scientific management. The Project Anillo has played a fundamental role in the education of students and young researchers. During its development 23 undergraduate students have worked in their title project and research, as well as 4 masters and 11 doctoral students have done their thesis. In addition, 4 doctors are performing their postdoctoral training in our Anillo. The tasks of training researchers has been strongly favored by the scientific exchange we made, both our trips to research group abroad (over 14), and the visits of professors and students from outside, where we received over 24 researchers, which allowed us to to establish new collaborations with groups of Universidad de Sevilla (Spain), Universidade Federal de Sao Carlos and Universidade Federal de Uberlandia (Bra- zil), Harvard University and University of Pittsburgh (USA), University of Antioquia (Colombia), ICIMAF (Cuba), University of Chihuahua (Mexico), University of Udine (Italy), KTH (Sweden), Fraunhoffer Institute (Germany), which adds to our former links to U. Califormia Southern, Flori- da International University, Iowa State University and the National Cancer Institute in the USA, Uppsala University in Sweden, U. Sao Paulo, Brazil, CNRS-University of Nancy in France. Outreach activities have been on two levels: technical meetings for specific audiences, as well as activities for public at large. In the first area, we highlight the organization of 14 schools and workshops, including 4 of an international character: Latin American School of Computational Materials Science (www.gnm.cl / school), together ICTP Italy, in Santiago (2008), Advanced Course on Free Energy Calculations: Theory and Practice, together Action Grid FP7 of the EC, in Talca (2009). Also, we co-organized two international conferences: Computing modeling and data driven: Y Symposium at the 11th International Conference on Advanced Materials, ICAM09 in Rio de Janeiro, 2009, and the First International Conference on Bioinformatics (SoIBio) in Chillan, 2010. Besides these, we have been invited as speakers in 16 international and 6 national events, and have presented papers and posters in 31 international and 42 national events, as well as more than 12 conferences and seminars in different universities of the country and abroad. Regarding the outreach to the public at large, our researchers and students have made over 10 activities, from lectures in colleges and schools, exhibitions to open house activities, reaching more than 1500 people across the country. We have also appeared on radio, television and interviews on printed media, describing our scientific work. Finally, it is interesting to note that our research activities have allowed us naturally to establish interaction with the productive sector, in a couple of initiatives that we are sure are just the beginning of a more regular basis. In fact, we worked with a company of the mining sector in the project Thermophysical Properties of mining tires, to optimize their use in trucks, us performing the simulations and the advice at field tests. On the other hand, together with the Faculty of Agronomy and the Institute of Chemistry of the U. Talca we are working on the project Nanobiology applied to the food industry, which has the support of the Fraunhoffer Institute and local businesses. Also, we are participanting in the education area, through the project Collaborative learning besed in growing infrastructure of GRID, in collaboration with the Bioinformatics group at PUC, Foundation for Life Sciences and the support from Microsoft-Chile, HP and Coffe Business. All in all, we can say that the support of the Bicentennial Program through the Project Anillo over these years has been the mainstay of our research groups, vital in joining together, consolidate and project them forward. III. RESUMEN EJECUTIVO

El Proyecto Anillo ACT-24 se titula Laboratorio de simulacióncomputacional de nanobio sistemas y su objetivo principal en investigaciónera a) el estudio de propiedades estructurales, dinámicas, mecánicas, electrónicas, magnéticas y ópticasde nanomaterials y b) el estudio de sistemas biológicos como prote´ınas transmembranales (canales TRP) y mecanismo de reaccióncatal´ıtica en enzimas (PEPCK). Durante el desarrollo del proyecto surgieron nuevos temas de investigación,tales como el estudio de la interfase entre un material orgánico y un metal y ondas de choque e impactos a hipervelocidades. Estos estudios se realizaron por medio de simulacióncomputacional a nivel molecular, la cual ha probado ser una técnica muy útil en el estudio teórico de sistemas donde su escala de longitud y tiempo va desde lo atómico a lo nanoscópico y eventualmente a lo microscópico.Unido a esto, exploramos temas de carácter meto- dológico y técnico, como fue el desarrollo exitoso de un códigode dinámicamolecular, la instalación de un sistema de cómputo de alto rendimiento (304 cores), y una plataforma web de nanopart´ıcu- las. Los resultados de estas investigaciones no sólotienen interés desde un punto de vista básico, sino también estánen condiciones de ser aplicados en investigaciones de interés estratégico para el desarrollo del pa´ıs, en áreastales como nanotecnolog´ıay biotecnolog´ıa. El Anillo ACT-24 descansósobre dos pilares fundamentales: el Grupo de NanoMateriales, www.gnm.cl, del Departamento de F´ısica de la Facultad de Ciencias de la Universidad de Chi- le (GNM), y el Centro de Bioinformáticay SimulaciónMolecular, http://cbsm.utalca.cl/, de la Universidad de Talca (CBSM). La sinergia producida de esta uniónnos permitióampliar los temas de investigacióninicialmente planteados, as´ıcomo incursionar en áreasmásaplicadas e interacciones con el sector productivo, que de otra manera habr´ıasido imposible realizar. El Anillo comenzócon un núcleode tres investigadores titulares, tres asociados y un conjunto de colaboradores tanto de Chile como del exterior, as´ıcomo cerca de 10 estudiantes, desde pregrado hasta doctorado. Estos investigadores y estudiantes eran de Antofagasta, La Serena, Santiago, Talca, Valdivia y Puerto Montt, con colaboradores en Brasil, Francia, España,EE. UU, India, Italia, Japóny Suecia. A lo largo de los tres añosde actividades nuestra red de colaboradores creció,incorporándose 4 investigadores postdoctorales, 25 estudiantes de postgrado y de pregrado, asi como colaboradores del exterior. Durante todo el desarrollo del proyecto trabajamos impulsando tres áreasprincipales: in- vestigacióncient´ıfica, la formaciónde recursos humanos y la difusiónde los trabajos de investigación tanto público a especializado como general. Los principales resultados de investigación alcanzados, que se describen a continuacion, estánplasmados en los 56 papers (ISI) publicados, as´ıcomo en las másde 100 presentaciones en congresos y conferencias, ademásde los art´ıculos publicados en revistas de circulacióncontinental y nacional. En el tema de materiales nanoestructurados y propiedades del bulto, estudiamos las propiedades del óxido de aluminio en estado amorfo y su fase cristalina γ-Al2O3, desarrollan- do un modelo estructural que presenta un muy buen acuerdo con los experimentos, lo que nos permitiócuantificar el carácter iónico del enlace, as´ıcomo dilucidar el cambio de sus propiedades vibracionales a medida que la muestra es sometida a presión.En la misma l´ınea, estudiamos el compuesto CdTeOx, un material de importancia actual en la búsqueda de mayor eficiencia en celdas fotovoltaicas: utilizando cálculos de dinámicamolecular ab-initio sobre este compuesto en estado amorfo, pudimos correlacionar los espectros de emisiónde fotolectrones (XPS por sus siglas en inglés) obtenidos experimentalmente con la estructura. Otro material amorfo investigado fue el CuZr, aleaciónque forma un vidrio metálico, con variadas aplicaciones, por ejemplo como material estructural debido a sus excelentes propiedas mecánicas. El estudio de las propiedades mecánicas y elásticas de materiales es un tema que se puede abordar con gran precisiónmediante cálculos basado en mecánica cuántica. As´ı,realizamos un trabajo teórico-experimental sobre platino que permitiódeterminar constantes elásticas en un amplio rango de presiones del Pt sometido a alta presión, obteniendo un excelente acuerdo con los experimentos en aquellos puntos donde estos datos estándisponibles. Usando la misma técnica de cálculo, abordamos el estudio de las propiedades mecánicasde la hidroxiapatita y la fluorapatita, componentes claves del esmalte y cuerpo de los dientes. Otro tema de investigaciónfueron las propiedades de superficies e interfaces, tanto se- miconductoras como metálicas. Aqu´ırealizamos estudios de carácter básico, as´ıcomo aplicaciones a problemas concretos de f´ısica de materiales y sistemas biológicos,en estrecho contacto entre los investigadores del GNM (U. de Chile) y el CBSM (U. Talca). De este modo, sumando esfuerzos y experiencias, pudimos abordar problemas desde un punto teórico-experimental, en sistemas inorgánicos y orgánicos.En colaboracióncon investigadores de la Universidad de Sevilla estudiamos la adsorciónde átomosde oro en superficies nitrogenadas de anatasa, una variedad de óxido de titanio con propiedades fotocatal´ıticas,de gran interés actual en la búsquedade catalizadores estables y baratos que pueden ser activados por luz. Otro estudio de propiedades de superficie fue llevado a cabo junto a un grupo experimental de la U. de Chile: se estudió,en pel´ıculas delgadas de oro, la influencia de bordes en la conductividad eléctrica de la pel´ıcula.En el áreade interfaces entre sistemas metálicosy orgánicos, destacamos el estudio sobre la adsorcióndel oligopéptido RGD en dióxido de titanio. Este tópicotiene directa relacióncon la respuesta de los tejidos a los implantes de titanio, de gran uso actualmente en medicina, pues el óxido de titanio es la interface natural entre los tejidos y el titanio. En el campo de la biolog´ıaes también posible indentificar ciertas respuestas inmunológicasa través de interaciones entre estructuras atómicas de oro y prote´ınastales como la opsonina, fribronectina y otras. Para representar esto, modelamos un sistema donde interactúan clusters de oro con tioles, resultando que la interaccióndel compuesto orgánicoera energeticamente másestable en el estado desprotonado que en el protonado. Finalmente, otro estudio realizado tiene relacióncon la corrosiónde óxidos metálicos por ácidosorgánicos, un problema de importancia práctica tanto a nivel insdustrial como de laboratorio. En particular, estudiamos óxidos de cobre y de zinc atacados por ácido fórmico, encontrando a través calculos de mecánica cuántica que el cobre resiste mucho mejor, debido la interaccióndirecta entre el ox´ıgenoy el metal, a diferencia del zinc, que envuelve una capa hidroxilada y una molécula de agua.

(a) Molécula de aspartato sobre superficie de (b) AGS-FA-PAMAM-QDot en TiO2 célula tumoral

Figura 2: Ejemplos de interface metal-orgánicay puntos cuánticos-dendr´ımeros. Puntos cuánticos (quantum dots) fue un tema planteado desde los inicios, pero que pronto fue extendido a su interaccióncon sistemas orgánicos.Esto fue abordado en diferentes niveles de complejidad y aproximaciones. Uno de los estudios emprendidos estárelacionado con el compor- tamiento de un punto cuántico sometido a un campo magnéticovariable, usando la aproximación de masa efectiva. Del mismo modo, estudiamos las propiedades magneto-ópticadel semiconductor CdxZn1−xSe, demostrando que el recocido térmicoproduce evaporacion del Cd, modifica la forma del confinamiento cuántico y permite sintonizar sus propiedades magnéticas. Particularmente interesante es el estudio teórico-experimental emprendido en conjunto con el Instituto de Qu´ımica de la U. de Talca, respecto de la s´ıntesis y caracterizacióndel complejo punto cuántico-dendr´ımero, de gran importancia por su aplicaciónpara obtener imágenes de células tumorales. En efecto, tales son los progresos en esta investigación,que se ha podido realizar ya una primera prueba en el sistema de imageneolg´ıa celular, distinguiendo células tumorales de las sanas. Nanotubos de carbono (CNT) es otro tema planteado inicialmente, en particular su interac- cióncon moléculas y el posible uso como sensores. Primeramente estudiamos la absorciónde NH3, NO2,H2O y O2 sobre CNT que ten´ıan una vacancia doble y que podr´ıaactuar como sitio activo. Sin embargo, debido a una débilinteracciónde van der Waals, nuestro resultados sugieren que un CNT con estos defectos no es buen candidato para ser usado como sensor. Luego estudiamos las posiblidades del uso de CNT como materiales para almacenar hidrógeno,un tema candente debido a la búsqueda de nuevas fuentes y formas de energ´ıa. Las energ´ıas involucradas en el proceso de absorcióny desorpcióndel H2, calculadas en base a dinámicamolecular cuántica, sugieren que CNT con nanoporos producidos por irradiaciónpodr´ıanser usados con éxito como depósitos de hidrógeno.Otro de los proyectos abordados estudia las condiciones en que las porfirinas de hierro (FeP) se pegan a un CNT, y por tanto las posiblidades de usar un CNT como soporte para pegar macrociclos metálicosen su superficie, cuya actividad electrocatal´ıtica ha sido reportada experimentalmente. Nanomagnetismo, es decir, propiedades magnéticas de los nano-materiales es un tópico de gran importancia hoy d´ıa.En esta áreanuestra contribuciónradica en varios aspectos: desde estudios de propiedades dinámicasy térmicasde cadenas magnéticas (“nanohilos”) basados en simula- cióncomputacional de dinámica de espines, pasando por ferrofluidos, hasta estudios a nivel cuántico de adsorciónde nanoparticulas magnéticas (Fe13) en superficies de semiconductores, as´ıcomo la contribucióndel magnetismo no-colineal en la energ´ıa total del hierro a alta presión. En el estudio de sistemas biólogicos mediante simulacióncomputacional de gran escala nuestro Anillo ha realizado aportes significativos, ya sea en el aspecto metodológico,en la interpretaciónde experimentos y as´ıcomo en la predicciónde fenómenos, tales como diseño de drogas asistida por computador. En efecto, estudiamos canales iónicosde la membrana celular, tales como el canal de postasio K+. Esta importante prote´ına transmembranal juega un papel clave en la señal eléctrica de nuestro sistema nervioso, estáinvolucrada en enfermedades neuro- degenerativas y se sobre-expresa cuando se presentan ciertos cánceres, como el gástrico. Nuestra simulacióncomputacional a gran escala nos permitiócalcular la energ´ıa libre, determinar las propiedades estrcuturales y dinámicas de esta prote´ına, siendo capaces de interpretar la importancia funcional de dos aminoácidos claves que participan en el canal K+ activado. Del mismo modo, y en conjunto investigadores de la U. Valparaiso, logramos establecer el mecanismo electrostático usado en el transporte iónico a travésde esas membranas. El estudio de la catálisis enzimática representa otra aplicaciónexitosa de métodos computacionales a prote´ınas. Mediante el empleo de un esquema h´ıbrido que une mecánicamolecular y mecánicacuántica (QM/MM) estudiamos, junto a investigadores de la U. Santiago, los estados de transiciónen la reacciónde decarboxilaciónque ocurre en el sitio activo de la prote´ına PEPCK. Hemos analizado en detalle el rol que juegan dos metales que toma parte en la reaccióncatal´ıtica de la enzima PEPCK, as´ıcomo el proceso de deprotonización,cuestiónimposible de resolver por otros medios. El diseñode drogas asistido por computador tambiénfue un área de investigaciónexplo- rada por nuestro Anillo, donde nuevamente nuestra experiencia en el uso de distintas metodolog´ıas computacionales permitióafrontar con éxito varios problemas, principalmente asociado a las interacciones prote´ına–ligando. En efecto, mediante un método h´ıbrido QM/MM as´ıcomo otros técnicas, estudiamos interacciones no-covalentes (puente de hidrógeno)entre ligandos y sitios activos en ciertas prote´ınas kinasas, que participan en cáncer, Alzheimer y otras patolog´ıas.Por ejemplo, nuestros resultados muestran que la energ´ıaasociada al enlace puente de hidrógeno es la principal compo- nente de la interaccióne indentificamos los principales residuos involucrados en el potencial del compuesto. Siguiendo en la l´ıneade investigaciónen problemas biólogicos que pueden entenderse mejor a travésde un modelo a nivel molecular, abordamos el estudio de sistemas lejos del equilibrio. Hemos colaborado con médicos de la Cl´ınica Arauco en el estudio del efecto de ondas de choque en sistemas biólogicos. La motivacióncentral es el uso creciente de la terapia de ondas de choque en el tratamiento de fracturas y diversas heridas y el escaso conocimiento sobre la interacción de ellas con el tejido humano. Para contribuir en este aspecto, hemos simulado a nivel atómico, primeramente, los efectos de ondas de choque en sistemas inórganicos como un bloque de argón, describiendo en detalle el proceso de fractura que all´ıocurre. Unidos a estos esfuerzos, también nos interesa describir a nivel atómicoel dañoproducido por el impacto de pequeñosproyectiles en materia orgánica e inorgánica. Resultados promisorios en el caso de un nanoproyectil de cobre sobre un blanco nos permiten mirar con optimismo los resultados de esta l´ınea de investigación. Nuestras actividades no sólose traducen en resultados cientif´ıcos propiamente tal, sino también plataformas de trabajo e infraestrucura cient´ıficade alcance internacional. En este sentido, estamos orgullosos de dos logros: hemos creado una base de datos para nanobiolog´ıa, Collaboratory for Structural Nanobiology (http://nanobiology.utalca.cl/) y una suite para simulacióncomputacional llamada Las Palmeras Molecular Dynamics (www.lpmd.cl), ambos, hasta donde sabemos, las pri- meras de su género en latinoaméricay de categor´ıamundial. La base de datos Collaboratory for Structural Nanobiology ha sido desarrollada en conjunto con el Instituto Nacional del Cancer, EE. UU, y estáconcebida como un espacio para facilitar la interacciónentre los investigadores que tra- bajan en nano-biotecnolog´ıa, salud y medicina. El paquete computacional Las Palmeras Molecular Dynamics, que ha sido desarrollado complementa en nuestro Anillo, es un programa que permite la simulacióny visualizaciónde materiales a nivel atómico y molecular, liberado con licencia GPL. En cuanto a infraestructura cient´ıfica, destaca la creaciónde tres laboratorios: el laborario del Grupo de NanoMateriales, en la U. de Chile, y los laboratorios de ingenier´ıade prote´ınasy de microscop´ıaelectrónica en la U. de Talca. Junto a estos laboratorios, instalamos un Centro de computaciónde alto rendimiento, financiado en forma conjunta por nuestro Anillo y la U. Talca, que tiene un total de 308 cores interconectados con una red infiniband, ideal para cálculosen paralelo, en el cual hemos realizado la mayor´ıa de las simulaciones de gran escala. Asimismo, hemos istalado un cluster máspequeñoen la Universidad de Chile. El diseño,instalacióny puesta a punto de estos equipos a sido un esfuerzo mayor desde el punto de vista técnico y administrativo que nos ha dado una enorme experiencia de gestióncient´ıfica. El proyecto Anillo ha jugado un rol fundamental en la formacion de estudiantes e investigadores jóvenes. Durante su desarrollo han trabajado en su memoria y unidades de investigación 23 estudiantes de pregrado y han desarrollado sus tesis 4 estudiantes de magister y 11 estudiantes de doctorado. Además, 4 doctores realizan su entrenamiento postdoctoral en nuestro Anillo. Las tareas de formaciónde investigadores se ha visto fuertemente favorecidas por el intercambio cient´ıficoque hemos podido realizar, tanto de nuestras salidas a centros del exterior (másde 14), como visitas de profesores y estudiantes del exterior a nuestros laboratorios, donde hemos recibido a 24 investigadores, lo cual nos ha permitido establecer nuevas colaboraciones con grupos de la Universidad de Sevilla, Universidade Federal de Sao Carlos, Universidade Federal de Uberlandia, Harvard University, University of Pittsburgh, University of Antioquia, ICIMAF (Cuba), University of Chihuahua, University of Udine, KTH (Sweden), Fraunhoffer Institute, que se agregan a nuestros antiguos colaboradores de U. Southern Califormia y Florida International University en EE. UU, Uppsala University en Suecia, U. Sao Paulo, Brasil, CNRS-University of Nancy, Francia y National Cancer Institute de EE.UU. En cuanto difusiónde la actividad cient´ıfica,esta se ha dado en dos planos: encuentros técnicos para público especializados, as´ıcomo actividades para el público general. En el primer ámbito, destaca la organizaciónde 14 escuelas y workshops, 4 de ellos de carácter internacional: Latin Ame- rican School of Computational Materials Science (www.gnm.cl/school), en conjunto con el ICTP de Italy, en Santiago, 2008; Advanced Course on Free Energy Calculations: Theory and Practice, en conjunto con FP7 Action Grid de la CE, en Talca; tambiénco-organizamos otras dos conferencias internacionales: Computing modeling and data driven, Simposio Y de la 11th International Confe- rence on Advanced Materials, ICAM09, en Rio de Janeiro, 2009; y First International Conference on Bioinformatics (SoIBio), en Chillan, 2010. Junto a esto, hemos dado charlas invitados en 16 eventos internacionales y en 6 nacionales, y hemos presentado trabajos y posters en 31 eventos internacionales y en 42 nacionales, as´ıcomo másde 12 coloquios y seminarios en diferentes univer- sidades del pa´ısy exterior. Respecto de la difusióncient´ıfica a todo público, nuestros investigadores y estudiantes han realizado sobre 10 actividades, desde charlas en liceos y colegios, exposiones y actividaes de puertas abiertas, con llegada directa a másde 1500 personas a lo largo del pa´ıs. Tambiénhemos tenido comparencencias en la radio, televisióny en entrevistas en medios escritos, dando a conocer nuestro trabajo cient´ıfico. Finalmente, es interesante destacar que nuestras actividades de investigaciónnos han permitido interactuar de manera natural con el sector productivo, en un par de inciativas que, estamos seguros, son solo el comienzo de una relaciónmásregular. En efecto, hemos trabajado junto a una empresa del sector minero en el projecto Propiedades termof´ısicas de neumaticos mineros, para optimizar el uso de ellos en los camiones, haciendo nosotros las simulaciones y asesoramiento de las pruebas en terreno. Por otro lado, junto a la Facultad de Agronom´ıay el Instituto de Qu´ımica de la U. de Talca trabajamos en el proyecto Nanobiolog´ıaaplicada para la industria de alimentos, que cuenta con la ayuda del Instituto Fraunhoffer de Alemania y empresas locales. En el áreade educacióntambién estamos participando, a travésdel proyecto Aprendizaje colaborativo basado en infrestructura de GRID, junto al grupo de Bioinformáticade la PUC, Fundacion Ciencias para la Vida y el apoyo Microsoft-Chile, HP y Cofe Bussines. En definitiva, podemos decir que el apoyo del Programa Bicentenario a través de estos años, por medio del Proyecto Anillo, ha sido un pilar fundamental y decisivo para unir, consolidar, y proyectar hacia adelante a nuestros grupos de investigación. IV. RESULTS IN RESEARCH

The main results in research of our project consists in the ones about the proposed topics, a well as new topics that emerged during the development of the project. They are reflected in the more than 100 contributions to national and international conferences (see Section V) and in more than 60 published papers that are listed in Section VII. Here we will review only some of those results, stressing the novelty and interelation of the different topics. The areas considered in our original proposal, which has been consolidated as research topics in our groups thanks to this project, are: A ) physical properties of nanostructured materials (mechanics of nanomaterials, nanotubes, nanomagnetism, semiconductor nanoparticles), leaded by the U. Chile team and B) Molecular simulation (MD and QM/MM) of biological systems (transmembrane proteins, enzymatic catalysis and protein-ligand interactions) and structural characterization of dendrimers, leaded by the U. Talca team. Also, along this project we have developed other related areas that emerged during these years: C) nanobiology, computational drug design, metal-organic interfaces, shock waves in biological systems, hypervelocity impact, code development, among others. Most important, we have strengt- hened the research and academic links between the two teams thanks to these new topics. Thus, the synergy has specific results expressed as collaborations, mentoring of undergraduate and post- graduate thesis, postdoctoral fellows, as well as mobility of researchers and students. The scientific achievements can be also measured in the number of invitations at Plenary lectures, given in national and international conferences by almost all members of Project Anillo (see Sec.IV), the collaboration and scientific exchange with several group and colleagues around the world, as well as the organization of several international schools and simposia (see Sec.VIII). It is interesting to note that during these years, we have incorporated as collaborators several Phd. researchers and graduate student, from different universities, like Univ. Austral Valdivia, U. Tarapaca, U. Tec. Fedrico Santa Mar´ıa,Univ. Andres Bello, as well as as Postdoctoral Fellows (supported by a Fondecyt grant). In addition, colaboration arise with other Anillos team, like the one of Non-linear physics at Fac. Cs. Fis. y Mat-U. de Chile, leaded by Dr. E. Tirapegui and Dr .M. Clerc (Proyecto Anillo ACT-15), and Experimental Plasma Physics, P4, from CCHEN, leaded by Dr. L. Soto, (Proyecto Anillo ACT-26). In the next pages, we describe the main research activities developed, pointing out both, the success and the difficulties we experienced in the different projects. We will begin describing the research results on the topics proposed in our original proposal, and then the new ones.

A ) Physical properties of nanostructured materials

IV.1. Nanostructured and bulk materials In this area, the main efforts have been directed to simulated structural and mechanical properties of nanocrystalline materials. In this respect, and in order to have a complete domain over the simulation techniques and how to perform it according our needs, we have been developing a molecular dynamic program, as well as several tools to analyze the results. The outcome of this efforts is the Las Palmeras Molecular Dynamics (LPMD) package (http://www.lpmd.cl), developed mainly by PhD sutdents at GNM: S. Davis (KTH, Sweden, and member of GNM, now Fondecyt postdoctoral fellow at GNM.), J. Peralta and C. Loyola (both graduated in 2010 and now a postdoctoral fellow at Iowa State University), F. Gonzalez (current PhD student). LPMD is a molecular dynamics (MD) code written from scratch in C++, as user-friendly, modular and multiplatform as possible. Some of its features are: it is an Open Source code, it works using plugins, it reads simple and intuitive configuration files, and includes utility software to perform analysis, conversion, and visualization of MD simulations. Today, the stable branch 0.6 in its latest version is 0.6.1. This last version includes new features such as more friendly control files, more efficient simulation times, a new API version (2.0). On the latest tests, LPMD has shown good agreement with other software, but longer simulation times; an issue which we hope to improve in future releases. One of the aims for the next version is to optimize the linkedcell method, for better performance in more massive simulations. The Fig. 3 show the number of lines of C++ code, from the version 0.5.0 to the lastest stable version 0.6. We expect the future code lines increasing to be only in the plugins, consolidating the API code. The last stable version have in their distribution python-code lines. LPMD includes additional software to compute properties from previous simulations, such as Analyzer: for output files (from other software or LPMD itself), to obtain pair distribution function, angular distribution, coordination number, Common Neighbor Analysis, correlation, Density/Temperature Profiles. Converter: converts between different MD file formats: XYZ, POSCAR (VASP), CONFIG (DLPOLY), mol2, lpmd (LPMD). Visualizer: to animate MD simulations. See more detail in the web page www.lpmd.cl, and the recently published paper entitled Las Palmeras Molecular Dynamics: A Flexible and Modular Molecular Dynamics Code in Computer Physics Communications, Sec. VII [43].

(a) Number of lines of C++ code progress, from (b) Nanocrystal built with a utility the version 0.5.0 to the latest stable version of LPMD

Figura 3: LPMD package. Most of the incremental improvement has been in the plugins principally, consolidating the API code.

Other achievements in materials calculation have been:

molecular dynamics and X-ray photoelectron spectroscopy study of CdTeOx, was published (Sec.VII [29, 38, 39]). We obtained structural models for the amorphous materials a-CdTeOx, (0,2 < x < 3), using ab initio molecular dynamics, and we have made a detailed description of the variety of atomic environments found in these materials. These structural models, in the form of xyz coordinates of the atoms in a supercell, were used subsequently to calculate the XPS spectra and validate them by comparison with experimental data. the experimental and theoretical study of the strength of polycrystalline coarse-grained platinum to 330 GPa and of nanocrystalline platinum up to 70 GPa was done and published, Sec. VII [16]. amorphous alumina under pressure has been studied and a manuscript submitted to PRL. Referees recommend no to publish in PRL, but have a favorable opinion for another journal. We worked in that comment and submit it to PRB, Sec. VII [59]. amorphous alumina by ab-initio calculation has been studied and published in Sec. VII [45], and a detailed report has been submitted, Sec. VII [60]. amorphous germania under pressure has been studied and the results presented in several conferences (See Sec.IV [41, 43]). Two articles were published Sec. VII [22, 45] vibrational properties and infrared spectra and of γ−alumina were studied, and the results were presented in several conferences (See Sec. IV [40, 42, 47]) and published in one article Sec. VII [46]. In this work, the vibrational properties of the four available structural models of γ−alumina were computed, looking relatively similar. However, the simulated infrared spectra (depend on the dynamical dipole moments of the vbra- tional modes) show remarkable differences that could be observed in low temperature measurements. in the 2 months visit of PhD student C. Valencia from U. Antioquia we studied structural and dynamical properties of Cu46Zr54 bulk metallic glasses (BMG), a hot topic today because the unique mechanical properties of BMG. A paper has been published Sec. VII [50]. mechanical properties of Hydroxyapatite (HAP) and fluorapatite(FAP). Hydroxyapa- tite (HAP) is an essential components of dental enamel and bone, and the elastic properties of single crystal HAP are not know. Fluorapatite(FAP) is found in sick teeth (fluorosis) and degrades its mechanical resistance. We made a computational study of the elastic properties of HAP and FAP using ab initio and forcefield techniques. Our ab initio HAP stiffness constants differ from previous calculations, but follow similar trends. The pseudo single-crystal HAP experimental stiffness constants in current use are critically reviewed. Combining the data from the ab initio simulations with the experimental FAP stiffness constants, several new HAP stiffness constants are proposed. We found that the properties mismatch between HAP and FAP is evidently too small to assume it directly responsible for the dental enamel mechanical degradation with fluorosis desease. One article has been accepted (Sec. VII [56]).

IV.2. Semiconductors: surfaces, interfaces, quantum dots Several research projects have been conducted in this area, mainly leaded by E. Menendez. Among them: in collaboration with a team of the University of Sevilla (Prof. Fernandez-Sanz), we have studied the adsorption of gold atoms on nitrogenated surfaces of anatase, a polymorph of titanium dioxide with photocatalytic properties. Nitrogenation and deposition of transition metal atoms is an active line of research, oriented to find stable and cheap photocatalysts that are activated with visible light. The manuscript recently accepted (Sec. VII [55]). we contributed to a study of magneto-optical properties of CdxZn1−xSe semiconductor quantum dots, demonstrating that thermal annealing produce the evaporation of Cd material, modifies the shape of the quantum confinement and allows to tune magnetic properties. This a collaboration between six institutions in Brazil, Chile, France, and Germany. Our role was the ab initio calculation of the strain effects in the quantum dots and analysis and support the zincblende lattice model of the quantum dots. Besides, the work includes high quality experiments and multiband effective mass calculations of excitons states. An article was recently published, Sec. VII [41]. the study of Schottky barriers in the CdSe/Au interface, was cancelled. After submitting one article during the first year of the project, one referee asked to do tests of convergence with the size of the model system. The subsequent calculations revealed an artificial electric field across the interface which makes impossible to fit a barrier height. Several alternatives have been tried to eliminate this artifact, but none proved to be effective. we did calculation of the potential energy barrier in a model of grain boundary in gold nanofilms. This work, in collaboration with an experimental group at U. of Chile, consisted on an ab initio calculation of the potential barrier associated with a twin grain boundary identified with the help TEM images by the experimental group. This would be an input for a phenomenological theory of conductivity limited by grain borders. A talk was given in a group meeting and a report was written (Sec.IV[19]), and although, regretfully, the ab initio calculation revealed that for a twin boundary there is no potential barrier, this project is the beginning of a collaboration between a theoretical and experimental groups of our University, an important issue for both groups. we studied quantum dots at several levels of complexity and approximation. In one study, Sec.VII[4], using the effective mass approximation, we have studied the dynamical behavior of a quantum dot under variable magnetic fields. The subproject of electron-phonon coupled states in quantum dots nanocrystals, stated in the original projects for the first two years, was cancelled. This subproject had been delayed in benefit of arising collaborations with experimental groups. The experimental work on quantum dots was made by the group of Talca and is described below. In support of the experiments, we tried to establish good methods to calculate the structural and electronic properties with quantum mechanical atomistic methods. In particular, we wanted to study quantum dot phenomena related to their surface functionalization. Regretfully we obtained poor performance of the semiempirical methods (PM3,PM6,CNDOL) and extremely long computation times (for our cluster) with the DFT methods. IV.3. Nanotubes The interaction of carbon nanotubes (CNTs) with molecules and their possible use as sensors was one of our proposed works. We studied the adsorption of NH3, NO2,H2O and O2 onto a semiconducting CNT containing a divacancy, assumed as a possible active site. In general, we observe weak Van der Waals interactions, which do not introduce significant electronic perturbations in the CNT band structure to alter conduction properties in the CNT. Thus, our results suggest that defective CNTs would not be able for sensor applications. In the original project, we also proposed to study the functionalization of CNT with polymers. However, the description of this system by first-principles calculations proved to be complex and very computational demanding which could not be initated because our computational facilities (the Anillo cluster) took a couple of year to be fully operational. The unsuccessful results and the delay in the cluster start off led us to redirect the project on CNTs looking for both interesting and less computational-demanding systems. After a search we decided to focus in two problems: catalysis and energy needs. Thus, we studied CNTs as hydrogen storage materials and as support to attach metallomacrocycles for solid-gas heterogeneous catalysis: (i) H2 storage inside single-walled carbon nanotubes: The interaction of hydrogen molecules with multivacancy defects in CNTs and their subsequent incorporation inside at room temperature were investigated by ab initio molecular dynamic simulations. We find endohedral binding energies for H2 close to those estimated optimal for a reversible adsorption-desorption process, suggesting that nanoporous CNTs as produced by electron irradiation could be an effective hydrogen storage medium, allowing the access to the CNT inner space. Storage capacity of about 4 wt % are estimated for a 11 A.˚ CNT, with the possibility to be increased for CNTs with larger diameters. One article has been published in this issue, Sec.VII[30]. (ii) Iron Porphyrin attached on carbon nanotube sidewalls: We explore covalent and non-covalent mechanisms to attach iron porphyrins (FeP) on the surface of single-walled carbon nanotubes (CNTs). We studied the stability and electronic properties of several FeP-CNT assemblies to shed light in the experimentally reported electrocatalytic activity of carbon-supported Fe macrocycles and the role of the linking structure. One article has been published in this issue, Sec. VII [40]. The catalytic activity of this supramolecular complex for the oxygen reduction reaction is currently under investigation. This work is part of the Ph.D. thesis of Igor Ruiz-Tagle at U. Andres Bello (UNAB) in Santiago under the supervision of W. Orellana. In other activities concerning the study of CNTs, we have collaborated with an international team in a research on excited states and optical properties of single walled carbon nanotubes. We have studied these properties using an approximate method to the Hartree- Fock self-consistent method and a subsequent configurations interaction calculation. One article has been published, Sec. VII [42]. The optical properties of several types of carbon nanotubes were studied and compared with high level ab initio calculations with satisfactory accuracy. The promise of this method is that, being computationally light, can be applied to a number of interesting phenomena related to finite and defective nanotubes, as well as in interaction with other nanostructures (Menendez and Orellana). IV.4. Nanomagnetism Several topics has been treated here, among them: Strongly interacting systems: we have studied the dynamical behavior of strongly interacting systems for few and large number of magnetic particles. In particular, for two, three, four and five particles we focus in different geometric configurations. In all this cases, the conservative dynamics present a rich types of behaviors such that transitions between chaos and regular motion depending on the parameters. In the case of large number of particles (N 100) we studied a chain geometric configuration. We explored both dissipative and conservative systems. We found that due to the dipolar interaction the absolute value of the total magnetization is not conserved, see Sec. VII [1, 9, 10]. Finally, the statistical mechanics properties for a large number of particles for different types of magnetic interactions were analyzed. Ferrofluids: we studied magnetic fluids formed by a stable colloidal suspension of magnetic nano-particles dispersed in a carrier liquid. Different types of carrier liquids were considered, such as Newtonian, Maxwellian and General Visco-elastic fluids. The main problem was the convection phenomenon. We also analyzed the influence of magne- tophoretic effect and the coupling between the concentration and magnetic effect in the rotating convective thresholds of the binary magnetic mixtures We showed that rotation stabilizes the convection produced by heat injection. Amplitudes equations were derivate close to the bifurcations. Some of these results can be found in Refs. Sec. VII [2, 31, 57]. Magnetic nanowires: another topic explored deals with the dynamical behaviors on quasi-reversal systems, where 1-D magnetic systems are typical examples. In particular, we derived a new amplitude equation for dissipative system under a parametrical forcing, Sec.VII [14, 32, 33]. In addition, we characterized a new type of localized structures and some spontaneous breaking of symmetry that can appear in these systems. This work was done in collaboration with Anillo Project ACT-15. Adsorption of magnetic nanoparticles on surfaces: We studied the electronic and magnetic properties of iron nanoparticles with 13 atoms (Fe13) adsorbed on self-organized 1D structures onto semiconducting surfaces. These 1D structures are bismuth dimers perfectly aligned on the Si(001) surfaces. The Bi lines are very long (> 1 nm) but only 0.63 nm wide, they form after Bi evaporation from Si(001) at above 450 C. Our goal with this project is to shed light on the possibility to contruct 1D magnetic nanowire on semiconducting surfaces using the Bi lines as template. Our results show that the Fe13 nanoparticles are strongly adsorbed between the Bi lines, with binding energies of about 5 eV, nucleating as nanowires along the Bi lines after the adsorption. This nanowire shows interesting properties like metallic half-metal behavior along the wire, having magnetic moment of 2.6 µB/Fe-atom. Additionally, it exhibits a magnetic bistability in the plane normal to the wire direction. The calculated Fe-nanowire magnetic anisotropy energy is found to be of 1.6 meV/Fe-atom. The article describing the above results is currently under preparation. Motivated by the interesting properties of surface-supported nanoparticles, we started another project in this issue, not consider in the original proposal. It deals with nanoparticles of noble metals (Au, Pd, Pt) adsorbed on metal-oxide surfaces [TiO2(110) and CeO2(111)] and their application in catalysis. The above systems have shown superior catalytic properties for important reactions like the oxygen reduction and the carbon monoxide oxidation. We are exploring the origin of such as catalytic properties (Orellana). Heat diffusion in spin chains: the thermodynamic properties magnetic chains in the micro-canonical ensemble Sec.VII [28] and in classical dipolar systems has also been done, including the heat transport in magnetic chains. In fact, in two Master thesis (F. Cuturrufo and E. Valdebenito) directed by G. Gutierrez have explored the validity of the Fourier law in the case of 1-D system with anisotropy and external magnetic field. Non-collinear magnetism: by non-collinear magnetism ab-initio methods, our associated R. Lizarraga and E. Holstrom from U. Austral have studied the high pressure phase of iron (Sec.VII [20]).

B) Molecular simulation (MD and QM/MM) of biological systems

IV.5. Large-scale Molecular simulation of K+ channels Potassium channels are undoubtedly one of the most enigmatic and more studied proteins in biophysics. These transmembrane proteins are the clue for electrical signals of our nervous system, as well as they are involved in several neurodegenerative diseases. Several studies have found that in some cancers, like gastric cancer, these proteins are over-expressed and probably have an important role in this disease. In the field of therapies pain relief the K+ channels are used as an important target for design of new anesthetics. U. Talca team (D. Gonzalez and students) has implemented and developed modern methods of molecular simulation that are applied successful to these kind proteins. The knowledge at an atomic level of the structural and dynamic properties of these systems has a high impact in scientific research, contributing with novel hypothesis and contributing with the implementation of more efficient experimental strategies in the search of the mechanisms related to the activation of these proteins (Sec.VII [23, 24]. Inportant progress was made in the implementation of advanced methods for evaluation of free energy and large scale molecular simulations of transmembrane proteins. K+ channels have very complex activation mechanisms which are constituted by structural motifs well conserved along each family, however they can not be necessarily identified from a simple sequence analysis. In this context we highlight works, published as articles of great impact, in which results from molecular simulations allowed us to reinterpret the functional importance of two key aminoacids participating in the sensed temperature TRPV1 K+ channel activation. One of them is described in detail in the paper entitled Dissection of the components for PIP2 Activation and thermosensation in TRP channels, published in Proceeding of the National Academy of Sciences (see Sec. VII [6]). In the same way, computational predictions based in the analysis of long molecular dynamics simulations allowed us to identify the aminoacids involved in the modulation of electrostatic potential, which regulates the pass of ions across the hSlo K+ channels. In this study, we performed a huge, both experimental and theoretical, effort to establish the electrostatic mechanism used in the ion transport across these transmembrane proteins. The aforementioned work was published in the prestigious Journal of General Physiology (Sec. VII [12]) and it was awarded, by the editorial committee, appearing in the cover of the journal. Both articles, are the product of a well coordinated and fruitful colaboration between the experimental group leaded by Dr. RamónLatorre from Universidad de Valparaso, and the modeling group leaded by Dr. Danilo Gonzalez from Universidad de Talca.

IV.6. Enzymatic Catalysis Another developed area of the Anillo has been the structural study of the transition states of the decarboxylation reaction that take place in the active site of the PEPCK protein. To conduct these studies, leaded by U. Talca team, we have implemented hybrid calculation methods like the quantum mechanics/molecular mechanics (QM/MM) scheme. The results obtained so far have allowed us to analyze in detail the role of two metals that take part of the catalytic reaction of this enzyme (Sec.VII [25, 17]). It also has allowed us to analyze transitory deprotonation processes that are not feasible to analyze by other means. The set of theoretical results have been discussed in detail with Dr. Emilio Cardemil from the University of Santiago, who is a well-known expert in this protein. This studies allowed to perform the undergraduate dissertations of Hector Urbina (2008), Xaviera Lopez (2009) and Romina Sepulveda (2010), bioinformatics engineering students at the U. Talca. Thus, the theoretical results have been also included in undergraduate and graduate thesis from Dr. Cardemils students.

IV.7. Quantum Dot-Dendrimer complex This area of research, with application in cancer cell imaging, bring together the expertise of U. Talca team (D. Gonzalez) and U. Chile team (E. Menendez) in the synthesis and structural characterization of Q Dots-dendrimer complexes, and we have the support from Dr. Leonardo Santos at Chemistry Institute of U. Talca, who kindly allow us to use his laboratory and facilities. In fact, Dr. Daniela Geraldo, a postdoc associated to UTalca group that has implemented the synthesis and characterization of quantum dots and dendrimers. It is important to highlight the signiﬁcant progress made in this area, where this multidisciplinary collaboration between Dr. Santos and CBSM has led to the ﬁrst test for cell imaging system to distinguish tumor cells from normal cells, Sec.VII[54] (see Figure).

IV.8. Protein-ligand interactions and computational assisted Drug Design 2008-2010: During this period, we developed and applied diverse methods for prediction of physical-chemistry properties useful in the study of quantitative structure activity rela- tionships. Methods such as CoMFA, CoMSIA and QSAR 3D were used in our research. That ﬁeld had an accelerated development in our group during 2008 due to the incorporation of Julio Caballero to the PhD program of Applied Sciences at U. Talca. Moreover, the implementation of hydrid calculation methods, like quantum mechanics/molecular mechanics (a) AGS-FA-PAMAM-QDot on tu- (b) Dendrimer model of PAMAM mor cells G4 interacting with ibuprofen. Drug delivery

Figura 4: Examples of QD-dendrimers and drug deliver research

(QM/MM) and ONIOM, has allowed us to study not only enzymatic reactions, but non covalent interactions (hydrogen bonds) between ligands and active site of some protein kinases participating in cancer, Alzheimer disease and other pathologies. It is worthy to say that these hybrid methods have became useful in the study of interaction energies between inhibitors and protein, which in turn has allowed to establish good structural-activity correlation, mainly in protein kinase systems. This research area is leaded by Dr. Jans Alzate-Morales, who was hired recently by UTalca after his postdoctoral stay research at CBSM. In a first study, the ONIOM method was applied to study the hydrogen bond interactions between some CDK2 inhibitors and various models of the active site in CDK2/CyclinA system. It was found that according with the models size, a good description of the molecular interactions inside the active site can be obtained. From best model, it was possible to obtain a reliable correlation between the total ONIOM energy and the biological activity reported for compounds studied. The results show that H-bond interaction energy is the principal component in this proteinligand interaction and residues Lys89 and Asp86 are essential for great potency of compound NU6102. The main results of this work were published in Chemical Physics Letters Journal, Sec.VII[26]. In a second work, we performed Comparative molecular field analysis (CoMFA) and QM/MM hybrid calculations on 9H- purine derivatives as CDK2 inhibitors. CoMFA was carried out to describe the activities of 78 analogues. The models were applied to a training set including 64 compounds. The best CoMFA model included steric and electrostatic fields, had a good Q2 value of 0.845, and adequately predicted the compounds contained in the test set. Furthermore, plots of the steric CoMFA field allowed conclusions to be drawn for the choice of suitable inhibitors. In addition, the dynamical behavior of compounds with 4- (aminosulfonyl)phenyl, 4-[(methylamino)sulfonyl]phenyl, 4-[(dimethylamino)sulfonyl]phenyl, and [3-methoxy-4-(aminosulfonyl)]phenyl groups at position 2 of the 9H-purine scaffold inside the CDK2 active site were analyzed by QM/MM calculations. The interactions of these compounds with residues Lys89, Asp86, and Ile10 were characterized, see Sec.VII[49]. This research area will be reinforced by recent FONDECYT project granted to Dr. Jans Alzate- Morales.

C) New topics: a synergy between U. Chile and U. Talca teams

IV.9. Metal-organic interfaces

(a) Aspartate molecule (asparte acid desprotona- (b) Cistein aminoacid interacting de) on a TiO2 (rutilo) surface with a defect on the bottom of Au 8 cluster

Figura 5: Metal-organics interfaces

IV.9.1. Biological oligopeptide (RGD) on titanium oxide surface We have studied the adsorption of aminoacids on surfaces of rutile, which is the most stable polymorph of titanium dioxide and the natural interface between titanium implants and biological tissues. This investigation was a joint effort of U. de Chile (E. Menendez) and U. Talca (J. Henriquez ) teams and produced two Bioinformatics Engineering thesis works (R. Urzua and J. Mansilla). The aim of this investigation was to elucidate the main interactions involved on the phenomenon of adsorption of the oligopeptide RGD, on titanium at a fundamental level, using the molecular simulation tools, such as quantum mechanics and minimization techniques. From the molecular mechanics minimization it was found that the RGD peptide was localized on a fibronectin protein loop (1TTF), orientated toward outside (water face), accordingly with those results, that sequence enabled interaction with the TiO2 surface. We have employed several quantum mechanical codes to study this interaction: MO- PAC, VASP, and SIESTA. We have found that MOPAC does not produce good geometries, at difference with a test of truly ab initio calculations with VASP and SIESTA. The energies of adsorption of Arginine, Aspartic Acid and Lysine were obtained using two ab initio electronic structure packages (VASP and SIESTA). The first part of this work consisted in determining the model system with the minimal number of atoms needed to obtain consistent results of adsortion energies. It was established in this work, that to model the TiO2 (110)¯ surface in interaction with water molecules, it is required minimum a supercell with 40 oxygen atoms and 20 titanium atoms, arranged in 15 atomic layers, keeping the bottom six layers with the atomic positions fixed at the ideal crystal positions. The atomic positions of the top layers are allowed to relax, and the fixed bottom layers simulate the effect of the underlying thick material. To model amino acid adsorption, the TiO2 surface unit cell must be replicate at least twice in the two surface directions. Our model is severely limited due to not considering the rest of the water molecules surrounding the amino acid in aqueous environment. The amino acids arginine and aspartic present charged states (by proton transfer) in conditions of neutral pH. These protonation states were included in the simulations, and produces a strong dependence of the adsorption energy with the size of the unit cell, which make the results untrustable. The electrostatic interaction must be screened by the presence of water, with is not included in the simulation. The inclusion of water can be done using a solvent model (using a different program) or include explicit water molecules, multiplying the computer resources need. The main result of this research line is the results on water adsorption energies and the advances toward a realistic model system for simulation of the RDG interaction with the TiO2 surface. The results are still contradictory and more research is needed before submitting a publication.

IV.9.2. Amino acid contained sulphur atoms on interaction with gold cluster In the biological ﬁeld is possible to characterize some immunological responses through interactions involving on gold atoms structures and proteins such as opsosines (serum protein that binds to microbes to facilitate their phagocytosis in macrophages), tumor necrosis fac- tor therapy of Aaurimune, ﬁbronectin, and so on. The aim of this investigation is to suggest a theoretical model about the main interaction of biological compound contained sulphur on gold cluster defects. Theoretical calculations were made on surface of Au cluster interacting to thiols compound. Computational chemistry was performed using the hybrid method B3LYP. The gold defects structures were modeling as cluster concepts. The studies showed the interaction of organic compounds with its unprotonated state on Au cluster energetically more stable than its protonated state. In the case of methionine, its structural feature, as mean: absence of sulphydryl group, the interaction with the metal surface was mediated by the electronic density of sulphur. This investigation also was done by J. Henriquez form U. Talca and E. Menendez U. Chile and it resulted in Bioinformatics Engineering thesis of Waldo Acevedo (graduated on March of 2009).

IV.9.3. Organics Acid on metallic oxides surfaces: Cu2O and ZnO The experimental evidence shows that zinc oxide and copper oxide can suﬀer corrosion by organic acid derivatives. This research is an eﬀort to explain the interaction involves on that kind system at molecular level and, in this way, give a characterization of the atmospheric corrosion process. The quantum mechanics calculations indicate that the interaction energy between the organic compound and metallic surface is stronger for Zinc that the copper. This could be due at the direct metal-oxygen interaction in the zinc case, while, on the copper case this interaction involves the hydroxylated layer and one molecular water. The energetic and hardness analysis show that contained Zinc system was more stable than the container copper one. In the other hand the Cu2O-formate system was harder than the ZnO-formate system, therefore, the Zn systems are more easily corroded by the organic acid than the copper (see Sec.VII [15]). IV.10. Shock wave simulation and hypervelocity impact

(a) Solid argon, simulated with (b) Water, simulated with NAMD LPMD package by C. Loyola package by D. Aguayo

Figura 6: Shock waves simulations

In recent years the use of extra-corporeal shock waves therapy (ESWT) in the treatment of different ailments in human beings have been steadily increasing since its first application in 1981. The success of these procedure has mostly depended on clinical evidence, because the scarcity of our knowledge of the interaction between shock waves and biological tissues at the molecular or functional level. In order to gain a fundamental understanding of the effects of shock waves on biological materials, a research project has been established in the Facultad de Ciencias, U. de Chile, with the participation of physicians at Arauco Salud Clinic and Facultad de Medicina, U. de Chile, researchers from U. Windsor (Dr. Aroca), Canada, and the Lab. of Raman spectroscopy, Dr. Campos and Clavijo) and GNM of Facultad de Ciencias, U. de Chile In this transdisciplinary project, our contribution shall be to simulate the behavior of this phenomenon at various levels of complexity. In addition, we have a Fondecyt postdoctoral fellow (Dr. Encina, Advisor: G. Gutierrez) working in this proposal. Also, we gave a course in the topic (see Sec.VIII, Course [9]). After a year of joint efforts of U. de Chile and U. Talca team, we have now some results. In the figure 6 we display pictures of the shock wave simulation on solid argon and in water. In both cases the methodology is similar: we assign to the piston certain velocity, generating a shockwave front. When the piston stop, a rarefaction wave developed, producing at the end the fail of the sample. In fact, in figure 6 we display three stage of this process: a) the shockwave advance just after the piston stopped. Note the clear difference between the high density shockwave front at one side (right) and the undisturbed material in the other side (left); b) the shockwave front is reaching the other extreme of the sample, developing a rarefaction wave behind it, and leaving a structure different to the initial fcc one; c) finally void growth can be seen. This study has been published in Computational Materials Science, Sec. VII [44], and form part of the PhD thesis of Claudia Loyola, at GNM. The research is conducted by PhD students at Santiago (solid argon) and at Talca (water), under direction of G. Gutierrez and D. Gonzalez respectivaly. Now we will continue in this line, introducing biological material, like proteins or membranes. Also, we have study the physics of hypervelocity impact, that is, collisions at velocity above sound velocity, between two nano-object (clusters). Preliminary results has been presented in seminars and Conferences Sec. IV [90, 91]. We stressed the fact that these projects, as well as the one on Quantum Dot-Dendrymer complex (see below, Sec.III.9), have enabled us to the develop new lines of research, where is needed the expertise both of the GNM team at U. de Chile and the CBSM team of U. Talca.

IV.11. Convection of polymeric solutions In this ﬁeld we have developed a model for convection polymer solutions in a liquid, such as DNA. We have shown that the eﬀect of rotation stabilizes the threshold of convection, see Sec.VII[2, 5].

IV.12. Structural database of Nanobiology From 2008 to date, U. Talca team signed a contract of a sole source (the first one in Latin America) on behalf of SAIC-NCI, USA, which allowed us to jointly develop databases of nanoparticle structures CNS. The beta version is available in http://nanobiology.utalca.cl/. At present we are working on molecular simulation protocols that enable us an efficient filling of that database. This work was key in the current colaboration between Fraunhofer Institute and UTalca team to develop the line research of NanoBiotechnology in Food.

IV.13. High performance computing facility One of our goal was the develpment of a top level scientific computer lab, and the final set up of a high performance computing system. After almost one and a half year of negotiation with Hewlett Packard, the high performance computing (HPC) system was finally installed on December 2008 at Universidad de Talca. The system consists of 38 blades, each one with 2 Quadcore Xeon processors, suming in total 304 cores. The nodes are interconnected with Infiniband (20 Gbps) and Gigabit Ethernet networks. The total investment on the computer system was $ 160 million pesos. The Anillo Project provided 65 million pesos (40 %) and the University of Talca made a contribution of 95 million pesos (60 %). Currently, the cluster is running with high production quotas, with a system of queues (PBS) that has responded properly to the demands of researchers and students associated to the scientific Anillo. Other notable achievement is the settlement of a physical space for the Group of Nano- materials at the University of Chile, which is on operation since April 2008. During 2008 we adquired a Dell computer with 4 Quadcore Xeon Processors that is being used for calculation. It had has an intermediate cost between the personal computers and the HPC of Talca. All this infrastructure now will be complemented with the CONICYT project for major equipment in HPC, titled “National Laboratory for High-Performance Computing (NLHPC)”. V. NATIONAL AND INTERNATIONAL COLLABORATION

Here we list the main activities related to increases the link and collaboration with other groups and researchers both at national and international level. Several of them have been supported by the Grant for International collaboration ACI-52, awarded by our Anillo at the beginning of 2008. In the activities, a highlight are the Invited talks at international Conferences.

Invited Talks, International Conferences

[1] G. Gutierrez, Thermophysical properties of novel ceramic, Invited Talk, USA- AirForce windows on science, AFOSR meeting, Arlington, USA, 11-17 May 2008. [2] G. Gutierrez, Computer simulations in amorphous compounds, Invited Talk, Interna- tional Conference Material Informatics and DFT, Oran, Algeria from 11 to 13 October 2008. [3] G. Gutierrez, Ab-initio molecular dynamics for amorphous alumina and spin dynamics for magnetic systems, Invited Talk, Latin American School in Computational Materials Science, ICTP-UChile-UNAB, Santiago, Enero2009. [4] E. Menendez, Ab initio molecular dynamics of CdTe oxides, Invited Talk, Latin Ame- rican School in Computational Materials Science, ICTP-UChile-UNAB, Santiago, Ja- nuary 2009. [5] D. Gonzalez, Invited Talk as Plenary Lecturer, Bioinforsalud, First European Commission-Funded Initiative to Analyze Biomedical Informatics, Grid Technologies and Nanoinformatics, PAIS, March 2009. [6] D. Gonzalez, Invited Talk as Plenary Lecturer, First Workshop for Proteomics in the New World. LNCC, Petropolis, Rio de Janeiro, Brazil May 12-16, 2008. [7] D. Gonzalez, Collaboratory for Structural Nanobiology: Nanoparticles database, Invited Talk as Plenary Lecturer, 6th Workshop of Computational Chemistry and Molecular Spectroscopy, October 21-24, 2008. Punta de Tralca, Chile May 12-16, 2008. [8] D. Gonzalez, Nanobiology -The Next Frontier for Molecular Simulations, Invited Talk, Latin American School in Computational Materials Science, ICTP-UChile-UNAB, San- tiago, Enero2009. [9] W. Orellana, Magnetic nanoestructures on semiconducting surfaces: First principles calculations, Invited Talk, 17 International Material Research Congress, Cancún,Méxi- co, (August 2008). [10] W. Orellana, Self-organized Fe nanowires on semiconducting surfaces, Invited Talk, Latin American School on Computational Material Science, ICTP-UChile-UNAB, San- tiago (January 2009). [11] D. Laroze, Dinámica de sistemas Quasi-reversibles, Invited Talk as Plenary Lecturer, Sociedad Boliviana de Fisica, SOBOFI, La Paz, Bolivia (Nov. 2008). [12] Gonzalo Gutierrez was invited for an Invited lecture at the symposium on Science and Engineering of Nanoscale Systems: Scientific Discovery through Advanced Computation and Experimental Validation at the 2009 International Conference on Computational & Experimental Engineering and Sciences, ICCES’09 , 8-13 April 2009, Phuket, Thailand. Did not go because force majeure. [13] Dr. J. Alzate participated in the first International Congress in Pharmaceutical, Bio- chemical and Biotechnological Sciences that will take place between 1 and 5 of June 2009 in the Santa Maria Catholic University, Arequipa, Peru. Plenary Lecture [14] G. Gutierrez: – Co-chair Simposio Y - Computational Modeling and Data Driven Materials Discovery, ICAM09 (11th International Conference on Advanced Materials), Rio de Janeiro, 20-25 de Septiembre 2009. – Invited speaker at III Workshop on Novel Methods for Electronic Structure Calculations, La Plata, Argentina, 14-16 de octubre 2009. See http://congresos.unlp.edu.ar/index.php/NMESC/ [15] W .Orellana, invited speaker at Simposio Y - Computational Modeling and Data Driven Materials Discovery, ICAM09 (11th International Conference on Advanced Materials), Rio de Janeiro, 20-25 de Septiembre. [16] We note that E. Menendez also was invited as a Speaker at ICAM2009 and at III Workshop on Novel Methods for Electronic Structure Calculations, but he can not go for personal reasons.

Invited Talks, National Conferences

[17] G. Gutierrez, Heat transport in magnetic sytems, Invited Talk, Tópicos en F´ısicaNo Lineal, Santiago, Chile (Oct. 2008) [18] D. Laroze, Localized waves in magnetic wires, Invited Talk, Tópicosen F´ısicaNo Lineal, Santiago, Chile (Oct. 2008) [19] E. Menendez, Potential energy barrier in models of grain boundary in gold, Meeting of the Group of Nanotechnology of the Faculty of Physical and Mathematical Sciences of the Univ of Chile. 16 October 2008. [20] D. Laroze, Modelos extendidos en dinámica de Poblaciones: Efectos del Ruido, Invited Talk, Taller de Arqueolog´ıaMatemática,Arica, Chile, Oct. 2008. [21] D. Laroze, Magnetoconveccion no lineal, Invited Talk, Mini-Workshop Nucleo Milenio ?Magnetismo básico y aplicado, Reñaca, Chile. [22] E. Menendez, Calculo de barrera de potencial en intercaras metal semi–conductor por metodos de primeros principios, Invited Talk, II Escuela de Nanoestructuras, Valpa- ra´ıso, Chile, Jan. 2009.

Contributed talks and posters, International Conferences

[23] O. Suarez, P. Vargas, D. Laroze, Scaling of Magnetic phases as function of length in 1D linear Chain, CLACSA XIII, Santa Marta, Colombia (Dic. 2007) [24] W. Orellana, Fe adatoms along Bi nanolines on H/Si(001): Patterning atomic magnetic chain, 13th Brazilian Workshop of Semiconductor Physics Sao Paulo, Brazil (Abril 2007) [25] D. Holmes, F. González-Nilo, S. Brauchi, R. Latorre, M.I. Niemeyer, F. Sepulveda, an Science Paradigm for Latin America. 3rd IEEE Internacional Conference on e-Science and Gris Computing, Virtual Institute for Integrative Biology (VIIB):Belgrado, India, (Dic. 2007) [26] F. Gonzalez-Nilo, Charla plenaria titulada: Biomolecular simulations and structure bioinformatics of transmembrane protein: K+ channels. international workshop on collaborative bioinformatics EMBnet- RIBCentro de Bioinformáticay Simulación Mo- lecular, Malaga, España, (Junio 2007) [27] H. Digenova, A. Ruiz-Lara S. F.D.Gonzalez-Nilo, Structural analysis: Guanine Nucleo- tide Dissociation (GDI), in Solanum chilense (tomato). Mendoza, Argentina (2007) [28] C. Avila, F.D. Gonzalez-Nilo, R. Chehin, Blind docking studies of phosphatydil-serine to Glyceraldehyde-3-phosphate dehydrogenase, Dpto Bioqu´ımicade la Nutrición,Uni- versidad Nacional de Tucuman, san Miguel de Tucuman, Argentina (2007) [29] R. E. Cachau, M. J. Fritts, I. Topol, S. K. Burt, F. D. Gonzalez-Nilo, M. Matties, New modeling strategies for the computational characterization of nanobioparticles. Biophysical society-51th annual meeting, Baltimore, EEUU. (Marzo 2007) [30] F. D. Gonzalez-Nilo, M. I. Niemeyer, L. Zúñiga, W. Gonzalez, P. L. Cid, F. V. Sepul- veda. Neutralization of a single arginine residue gates open a two-pore domain, alkali- activated K+ channel. Biophysical society-51th annual meeting, Baltimore, EEUU. (Marzo 2007) [31] G. Orta, M. Salazar, W. Gonzalez, C. Mascayano, N. Raddatz, E. Rosenmann, F. Gonzalez-Nilo, S. Brauchi, R. Latorre. Dissecting phosphatidylinositol 4,5- bisphosphate activation and thermosensation in Trp channels.Biophysical society-51th annual meeting, Baltimore, EEUU. (Marzo, 2007) [32] I. Carvacho, W. González,P. Orio, S. Brauchi, O. Alvarez, F. D. González-Nilo, R. Latorre. External surface charge neutralization induces outward rectification on the Calcium- and Voltage- activated potassium channel BK. [33] J. Henr´ıquez-Román,C. Leygraf , H. Gil. A model of the interaction betweenorganic acid ion with oxidized metallic surfaces in presence of water molecules, Electronic Stated and Excitation on nanostructures. PASI-2007 Pan American Advanced Study Institute 2007. Zacatecas, Mexico, (Junio 2007) [34] W. Orellana, Stability of finite single-walled carbon nanotubes adsorbed on Si(001), American Physical Society Meeting, New Orleans, (Marzo 2008) [35] G. Gutiérrez,High pressure behavior of amorphous Al2O3: a molecular dynamics study, NanoTech 2007, Santa Clara, EE. UU, Mayo 2007. [36] G. Gutiérrez, S. Davis, Structural, dynamic and electronic properties of amorphous Al2O3: abinitio molecular dynamics calculations, American Physical Society Meeting, New Orleans, (Marzo 2008) [37] G. Gutiérrez,E. Valdebenito, S. Davis, Heat diffusion in a classical Heisenberg chain, American Physical Society Meeting, New Orleans, (Marzo 2008) [38] W. Orellana, Fe-porphyrins attached to single-walled carbon nanotubes: Electronic and dynamical properties from ab initio calculations. IFSC Universidade de SãoPaulo, Brazil, August 2010. [39] W. Orellana, Fe-porphyrins adsorbed on single-walled carbon nanotubes for heterogeneous catalysis. American Physical Society 2010 March Meeting. Portland, USA, March 2010. [40] Vibrational properties of gamma alumina, con C. Loyola y E. Menéndez, poster en CCP5 “Methods in Molecular Simulation Summer School 2008”(http://www.ccp5.ac.uk/SSCCP5/main.html) del 6-15 de julio de 2008 en Sheffield, Inglaterra. [41] Germania under pressure, con J. Peralta, poster en CCP5 ”Methods in Molecular Simulation Summer School 2008”(http://www.ccp5.ac.ukgxz/SSCCP5/main.html) del 6-15 de julio de 2008 en Sheffield, Inglaterra. [42] Vibrational properties of gamma alumina, con C. Loyola y E. Menéndez,poster en 29th International Conference on the Physics of Semiconductor, del 21 julio al 1 de Agosto 2008 en Rio de Janeiro, Brasil (http://www.icps2008.org). [43] Germania under pressure, con J. Peralta, poster en 29th International Conference on the Physics of Semiconductor, del 21 julio al 1 de Agosto 2008 en Rio de Janeiro, Brasil (http://www.icps2008.org) [44] Ab-initio molecular dynamics study of amorphous CdTeOx alloys, poster presentada por E. Menéndezen 29th International Conference on the Physics of Semiconductor, del 21 julio al 1 de Agosto 2008 en Rio de Janeiro, Brasil (http://www.icps2008.org) [45] Ab initio study of Au/CdSe Schottky barriers, poster, Menéndezen 29th International Conference on the Physics of Semiconductor, del 21 julio al 1 de Agosto 2008 en Rio de Janeiro, Brasil (http://www.icps2008.org) [46] Germania under pressure, con J. Peralta, Poster en Latin American School in Compu- tational Materials Science, ICTP-UChile-UNAB, Santiago, Enero2009. [47] Vibrational properties of gamma alumina, con C. Loyola y E. Menendez, Poster en Latin American School in Computational Materials Science, ICTP-UChile-UNAB, Santiago, Enero2009. [48] W. Orellana, Stability and bonding properties of finite single-walled carbon nanotubes adsorbed on Si(001). 6th Workshop of Computational Chemistry and Molecular Spectroscopy, Punta de Tralca, Chile, (October 2008). [49] W. Orellana, Fe13 clusters adsorbed along Bi nanolines on H/Si(001), 19 International Conference on the Physics of Semiconductors, Rio de Janeiro, Brazil, (August 2008). [50] Igor Ruiz-Tagle and W. Orellana, Theoretical investigation of Fe-phthalocyanine and Fe-porphyrin adsorbed on single-wall carbon nanotubes. 6th Workshop of Computatio- nal Chemistry and Molecular Spectroscopy, Punta de Tralca, Chile, (October 2008). [51] D. Laroze, J. Martinez-Mardones, Amplitude equation for stationary convection in a viscoelastic magnetic fluid. MEDYFINOL08, Punta del Este, Uruguay. (Talk) [52] M. G. Clerc, S. Coulibaly, D. Laroze, Dynamical Behavior of a magnetic wire. MEDY- FINOL08, Punta del Este, Uruguay. (Poster) [53] P. Diaz, D. Laroze, L.M. Perez, Configurational Temperature for a Dipolar Magnetic Chain. MEDYFINOL08, Punta del Este, Uruguay. (Poster)

Contributed talks and posters, National Conferences

[54] D. Laroze, L.M.Pérez, P. Diaz, Classical Spin Dynamics of four in interacting magnetic particles on a square LAWNP07, Arica, Chile (Oct. 2007) [55] D. Laroze, A. Toloza, C. Mendoza, J. Mart´ınez-Mardones. Amplitude equation for stationary convection in a rotating binary ferrofluid LAWNP07, Arica, Chile (Oct. 2007) [56] M. G. Clerc, S. Coulibaly and D. Laroze, Amplitude equation for a parametrically forced magnetic wire LAWNP07, Arica, Chile (Oct. 2007) [57] M. G. Clerc, S. Coulibaly and D. Laroze, Localized states beyond asymptotic parametrically driven amplitude equation LAWNP07, Arica, Chile (Oct. 2007) [58] G. Agüero, G. Gutiérrez,D. Laroze, G. Sánchez, Transferencia de Calor entre dos sólidos con geometr´ıacil´ındrica,Emfimin07, Santiago, Chile (Nov. 2007). [59] M. G. Clerc, S. Coulibaly, P. Diaz, D. Laroze and L.M. Perez, Dynamical Behavior of magnetic system Instabilities and Nonequilibrium Structures XI, Viñadel Mar, Chile (Dic. 2007) [60] M. G. Clerc, S. Coulibaly and D. Laroze, Localized states beyond asymptotic parametrically driven amplitude equation Instabilities and Nonequilibrium Structures XI, Viñadel Mar, Chile (Dic. 2007) [61] P. Diaz, D. Laroze, L.M.Pérez,Classical Spin Dynamics of four in interacting magnetic particles on a square Instabilities and Nonequilibrium Structures XI, Viñadel Mar, Chile (Dic. 2007) [62] D. Laroze, Localization and domain wall in magnetic wires, Mini workshop on Magne- tism, Reñaca, Chile (Abr. 2008) [63] W. Orellana, Structural and electronic properties of nanostructures from ab initio, Workshop on Free Energy Calculations Applied to Biomolecules, Talca, Chile (Nov. 2007) [64] W. Orellana, Estabilidad y propiedades de enlace de nanotubos de carbono de una pared depositados sobre la superficie de silicio (001), VI Encuentro de Modelos F´ısicos y Matemáticos en Ingenier´ıa,Santiago, Chile (Nov. 2007). [65] M. Vidal, H. Urbina, W. Gonzalez, I. Carvacho, y R. Latorre, F. Gonzalez-Nilo, Cavi- dad intracelular del canal de potasio Hslo: rol de residuos hidrofobicos en la conductancia de iones potasio. XXX ReuniónAnual de la Sociedad de Bioqu´ımica y Biolog´ıa Molecular de Chile. Chillán,Chile. (Sep. 2007). [66] D. Genova, F. Gonzalez-Nilo Fernando, F. Sepúlveda, M.Niemeyer, Análisis Termo- dinámico del Sensor de pH Presente en el Canal de Potasio task-2. XXX Reunión Anual de la Sociedad de Bioqu´ımicay Biolog´ıaMolecular de Chile. Chillán,CHILE (Sep. 2007). [67] H. Urbina, I.Tobar, Cardemil, F. Gonzalez, Rol Estructural del Residuo R457 en la afinidad de ADPDP en Carboxiquinasa Fosfoenolpiruvica de Saccharomyces Cerevi- siae. XXX Reunión anual de la Sociedad de Bioqu´ımicay Biolog´ıaMolecular de Chile. Chillán,Chile (Sep. 2007). [68] A. Vergara, H. Urbina, C. Gonzalez, M. Holmgren, F. Gonzalez-Nilo, Inactivacion del Canal de Potasio Shaker. XXX ReuniónAnual de la Sociedad de Bioqu´ımica y Biolog´ıa Molecular de Chile. Chillán,Chile (Sep. 2007). [69] C. Navarro, H. Urbina, T. Bar-Magen, C. Mascayano, J. Patton, F. Gonzalez-Nilo Re- conocimiento de RNA en RNA Polimerasa de Rotavirus RNA-Dependiente. Dinamica Molecular Dirigida y Simulación de Acoplamiento. XXX Reunión Anual de la Sociedad de Bioqu´ımica y Biolog´ıaMolecular de Chile. Chillán, Chile (Sep. 2007). [70] F. González Nilo Base de datos para estructura de Nanobiolog´ıa. IV Simposio Argentino-Chileno de Pol´ımeros. Viñadel Mar, Chile (Dic. 2007). [71] M. Saavedra, J. Caballero, F. GonzálezNilo. Estudio de interacción poli-e- caprolac- tona/ciclodextrina mediante SimulaciónMolecular. IV Simposio Argentino-Chileno de Polimeros. Viñadel Mar. Chile. (Dic.2007) [72] J. Caballero, F. GonzálezNilo. Estudio de la formación del complejo progesterona-b- ciclodextrina usando dinámica molecular dirigida. IV Simposio Argentino-Chileno de Polimeros. Viñadel Mar. Chile. (Dic.2007) [73] J. Henr´ıquez-Román, C. Leygraf, Interaction of carboxilate ion on Metallic oxided surface representation in presence of water molecules. XXVII Jornadas Chilenas de Quimica. Chillan, Chile. (Oct. 2007) [74] J. Henr´ıquez-Román, E. González,L. Padilla-Campos, M. A. Páez,Aminoácidos como inhibidores de la corrosiónde cobre en medio ácidoclorh´ıdrico. Una mirada experimental y teórica. XXVII Jornadas Chilenas de Qu´ımica.Chillan, Chile. (Oct. 2007) [75] E. Menéndez,Simulaciónde la estructura de vidrios de CdTeOx. VI Encuentro de Modelos F´ısicos y Matemáticos en Ingenier´ıa, Santiago, Chile (Nov. 2007) [76] C. Loyola, G. Gutiérrezy E. Menendez, Estudio a nivel atómicode las propiedades vibracionales de γ-Al2O3. VI Encuentro de Modelos F´ısicosy Matemáticos en Ingenier´ıa, Santiago, Chile (Nov. 2007) [77] J. Peralta, Las Palmeras Molecular Dynamics: DinámicaMolecular Flexible y Modula, VI Encuentro de Modelos F´ısicos y Matemáticos en Ingenier´ıa, Santiago, Chile (Nov. 2007) [78] E. Valdebenito, Transporte en sistemas magnéticos,VI Encuentro de Modelos F´ısicos y Matemáticos en Ingenier´ıa,Santiago, Chile (Nov. 2007) [79] G. Gutiérrez,C. Esparza, Cálculo de momentos de inercia mediante sumas finitas, XXI Congreso de Educaciónen Ingenier´ıa,SOCHEDI, Santiago, octubre 2007 [80] G. Gutiérrez, Estudio teórico de (nano)materiales, Encuentro de F´ısica teórico- experimental, FCFM, U. de Chile, Julio 2007 [81] G. Gutiérrez,Heat transfer in magnetic systems, Escuela de nanoestructuras, UTFSM, Valpara´ıso,Enero 2008 [82] Fractura de argónpor medio de ondas de choque, con C. Loyola, charla Simposio So- ciedad Chilena de F´ısica,Valpara´ıso,Nov. 2008. [83] Germania a altas presiones, con J. Peralta, poster en II Escuela de nanoestructuras, UTFSM, Valpara´ıso, Enero 2009.

[84] Structural and vibrational properties of amorphous GeO2 under pressure: a molecular dynamics study, con J. Peralta. Charla Simposio Sociedad Chilena de F´ısica, Valpa- ra´ıso, Nov. 2008. [85] D. Laroze, J. Martinez-Mardones, L. M Perez and Y. Rameshwar, Amplitude equation for stationary convection in a rotating binary ferrofluid, SOCHIFI08, Valparaiso, Chile. (Talk) [86] Cálculoy representacióngráfica de sumas finitas mediante gnuplot, con C. Esparza, XXII Congreso Chileno de Educaciónen Ingenier´ıa, La Serena, Octubre 2008. [87] Igor Ruiz-Tagle and W. Orellana, Theoretical investigation of Fe-phthalocyanine and Fe-porphyrin adsorbed on single-wall carbon nanotubes, XVI Simposio Chileno de Fi- sica, Valparaiso, (November 2008). [88] W. Orellana, Self-organized Fe nanowires on a semiconducting surface: Structural, electronic and magnetic properties from ab initio, XVI Simposio Chileno de F´ısica, Valparaiso, (Noviembre 2008).

[89] W. Orellana, G. Gutierrez, Stability and dynamical properties of Ti2SiC3(0001) at high temperatures: First-principles calculations. XVII Simposio Chileno de F´ısica,Pucón, Chile, Noviembre 2010. [90] C. Loyola, G. Gutiérrez, Impactos a hipervelocidad: simulaciónpor medio de dinámica molecular, [91] N. Amigo, C. Loyola, S. Davis, G. Gutiérrez, Impactos supersónicos de nano-proyectiles de cobre: un estudio mediante dinámica molecular, XVII Simposio Chileno de F´ısi- ca, Pucón, Chile, Noviembre 2010. XVII Simposio Chileno de F´ısica,Pucón, Chile, Noviembre 2010. [92] F. González-Cataldo, F. González-Wasaff, Y. Navarrete, G. Gutiérrez, Rebote de una esfera sobre una superficie: estudio a nivel atómico, XVII Simposio Chileno de F´ısica, Pucón,Chile, Noviembre 2010. [93] F. González-Cataldo, J. Peralta, C. Loyola, S. Davis, Visualización3D en tiempo real para dinámica molecular clásica: LPMD y LPVISUAL, XVII Simposio Chileno de F´ısica,Pucón, Chile, Noviembre 2010. [94] C. Rioseco, J. Rojas, N. Amigo, G. Gutiérrez,S. Davis, Estudio a nivel atómico de la colisióninelástica entre dos nano-objetos metálicos, XVII Simposio Chileno de F´ısica, Pucón,Chile, Noviembre 2010. [95] J. Peralta, G. Gutiérrez,W. Orellana, Propiedades elásticas y electrónicas del compues- to laminar Ti2GaN sometido a presión:estudio de primeros principios, XVII Simposio Chileno de F´ısica,Pucón,Chile, Noviembre 2010.

Visits from abroad and from other parts of Chile

[1] Prof. S. Saxena, de Florida International Univ, Marzo 2007 (1 semana), visita FC, Uch. [2] Dr. Norge Cruz, Universidad de Sevilla, España,Noviembre (4 semanas), visita FC, Uch. [3] Dr. Chris Chipot, CNRS, Nancy, Francia, Noviembre 2007 (1 semana). [4] Prof. R. Lagos, U. Estdual Paulista, Rio Claro, Brasil, Enero 2008 (1 semana), visita FC, Uch. [5] Visit of Sergio Davis, PhD student of the KTH, Sweden, and member of Group of Na- noMaterials. Sergio, who visited us in two opportunities, is one of the leader developers of the Las Palmeras MD package, and also help with cluster installation and gave a mi- nicourse of Python (NanoTaller de Python). June 2007, July 2008, and December2008- January 2009. Now, he is incorparated at GNM as a FONDECYT postdoc. [6] Visit of Prof. Carlos Camacho (University of Pittsburgh). Delivered a set of Lectures on Physics of Proteins from 11-14 August 2008, 4.5 hrs. 18 persons (PhD student, undergraduate and researchers) attended. Conversation on the topic of protein submitted under shock waves with Prof. G. Gutierrez and Dr. M. Brañes. [7] Visit of Prof. Roberto Miwa, Universidade Federal de Uberlandia, Brasil, from 29 Sept. - 3 Oct. 2008. Collaboration with Prof. W. Orellana on ab-initio calculation of metal- oxides surfaces. [8] Visit of Dr. Raul Cachau, National Cancer Institute-USA: 2 working visits at CBSB, U. Talca, November 14-20, 2008 and April 5 to 11, 2009. Both visits were related to the nanobiology project led by Prof. D. Gonzalez. From these visits, we expect the writing of at least 2 articles during the 2009 year and the co-tutor of 2 PhD theses and 2 or 3 under-graduate thesis. It has also initiated the development of a laboratory of crystallography of proteins and of electronic microscopy, both initiatives are provided with the support of the SAIC-NCI. [9] Visit of Prof. Giorgios Tsironis, Dept. Physics, University of Crete, Greece, from 11- 19 nov. 2008. Seminars at Dept. of Physics, Simposio Chilean Physical Society and conversations on topics of statistical physics. Possible collaboration on calculation of breathers in solid: Si, Ge by ab-initio calculations (see Appendix Sec.IV). [10] Visit of Camilo Valencia Balvin, PhD Student of the University of Antioquia, to acquire practice on Molecular dynamics calculation, under Prof. G. Gutierrez. See the report and the manuscript to be submitted on the topic of structural and dynamical properties of CuZr amorphous alloy . This visit is related to the one of Dr. Jorge Osorio-Guillen, and is the first step in our collaboration project. From Nov. 2008 to Jan 2009. [11] Visit of Prof. Jorge Osorio-Guillen, from Dept. Physics, Universidad de Antioquia, Medellin, Colombia, from 18-ene to 31 ene 2009. Participation in the Latinamerican School on Computational Materials Science as Invited Speaker and collaboration on bulk metallic glasses with G. Gutierrez. [12] Visit of Dr. Marcos Sotomayor, postdoctoral fellow at Harvard University, between December 12 and January 3, 2009. He taught courses Methods of Molecular Simulation, Advanced Course on Free Energy Calculations. Theory and Practice at CBSM-Talca. Additionally, he discussed cooperation issues. The course took 45 hours, 5 days. Dr. Sotomayor also gave a lecture on Protein Mechanics at the Group of NanoMaterials, Universidad de Chile., 28 Dec. 2008. [13] Dr. Chris Chipot came from Universite de Nancy, France, between December 12 and 19 of 2008. He taught courses Methods of Molecular Simulation, Advance Course on Free Energy Calculation: Theory and Practice at CBSM-Talca. The course had 45 hours, 5 days. During the visit of Dr. Chipot coordinated two under-graduate thesis and two research units for students of the Ph.D. program in Applied Science. [14] Visit of Javier Fernandez Sanz, University of Seville. This is a long term collaboration, initiated in 2005, with Prof. E. Menendez, and presently focused on the computation of surface and interface properties. He also gave a lecture at the Latinamerican School on Computational Materials Science as Invited Speaker. [15] Visit of Profs. Dr. E. Holstrom and Dr. R. Lizarraga of Universidad Austral at Valdivia, to U. of Chile. 18-24 de enero 2009. They are now permanent collaborators of our Project Anillo, and together Prof. Menendez, are working with Prof. A. Amezaga on alculation of XPS spectra (see below). . [16] Visits of Prof A. Amezaga, from Universidad Austral at Puerto Montt. Work on the calculation of core level shifts with Prof. Menendez. He is a permanent collaborator of the Anillo, and plan to begin his PhD studies at Universidad de Chile. He is coming to Santiago twice a month. [17] Visit of M. C. Alexander Odriazola Diaz, researcher at the Instituto de Cibernetica, Matematica y Fisica de Cuba from 2 April- 30 May, to work on Raman calculation of semiconductor quantum dots with Professor Eduardo Menendez. [18] Dr. Norge Cruz, de la Universidad de Sevilla, España,6-15 de november de 2009. Gave a short course on Methods for Materials Simulations, and woerked on topics of impurities in titanium dioxide surfaces and aminoacid desposited on the same surfaces. [19] Dr. Jorge Kohanoff, (http://titus.phy.qub.ac.uk/group/Jorge ) University of Belfast. 17-21 August 2009. He taught a short course “Simplified methods in electronic structure calculations”. The content of this course is the Chapter 10 of his book “Electronic structure calculations for Solids”. [20] Dr. Volker Eyert, del Center for Electronic Correlations and Magnetism, Institute for Physics, University of Augsburg, week 28 de September 2009. Talk: All-Electron Full- Potential Calculations at O(ASA) Speed. [21] Dr. Luis Montero, Faculty of Chemitry, University of Havana, 28/mar/2010- 3/abr/2010. This visit is related with the work on electronic structure calculations in large molecules and nanostructures using approximate semi empirical wavefunction methods (CNDOL). He gave talk to the group of nanomaterials and discussed topics on the calculations of uantum dots. [22] Dr. Jose Manuel Garcia de La Vega, Faculty of Science, Autonomous University of Madrid 30/mar/2010 al 2/abr/2010. This visit is related to the visit of Dr. Montero. Both visits were supported by an external project of international cooperatiion. He gave a talk to the Department of Physics. [23] Dra. Maria E. Fuentes, Fac. Chemistry, Autonomous University of Chihuahua, Mexi- co. 28/mar/2010-5/abr/2010. Related to the visits of Drs. Montero and Garcia de la Vega. Also worked on the properties of hydroxiapatite, and simulations of ferroelectric materials. [24] Dr. Alain Delgado Gran. Centro de Estudios Aplicados al Desarrollo Nuclear, Cuba. 28/ene/2010-8/mar/2010. We came to make applications of the CNDOL method to the electronic structure of quantum dots. His visit was supported partially by the Anillo and by a grant from the Thirld World Academy of Sciences (http://www.twas.org).

Research visits to other institutions

[1] G. Gutiérrez,visited the Collaboratory for Advanced Computing and Simulations (CACS), University of Southern California, May 2007. [2] E. Menéndez, Universidad de Sevilla, Octubre 2007. He was invited under a project managed in Sevilla from the Agencia Española de Cooperación Internacional. In this occasion he engaged in a research on impurities in a titanium dioxide crystal. [3] G. Gutiérrez y W. Orellana, Cesmec, FIU, Marzo 2008 [4] Prof. D. Gonzalez was invited by Ministry of Education and Science of Germany to attend to HannoverMesse 2008, showcase for industrial technology, Hannover, Germany and also is member of the commission for collaboration Chile-NCI of ministry of Health of Chile. [5] Dr. J. Alzate was invited by Ministry of Education and Science of Germany to attend to HannoverMesse 2009, showcase for industrial technology, Hannover, Germany that took place during the recent month of April. [6] Prof. E. Menendez visited the group of Prof. Javier Fernandez Sanz, Department of Physical Chemistry, University of Sevilla. This is a long term collaboration initiated in 2005, and presently focused on the computation of surface and interface properties, particularly, working on the calculation of Schottky barrier heights. 23/nov to 22/dec of 2008. [7] Prof. E. Menendez visited Prof. M. E. Fuentes Montero, at the University of Chihuahua, from 12 to 25 Feb 2009. The program consisted in teaching a tutorial course on the simulation package Quantum-ESPRESSO and to explore cooperation in topics of materials science. From this visit the following lines appeared as cooperation projects to be delivered in the next year: Computation of elastic properties of hydroxyapatite. This is a mineral that composes most the bones and dental enamel. Computation of excited states and optical properties of carbon nanotubes and quantum dots using quantum chemistry semi-empirical methods. [8] Prof. E. Menendez visited the Autonomous University of Madrid, from 27/january to 3 February 2010. He visited the group of Prof. Jose Garc´ıade la Vega in the framework of the project of computation of excited states and optical properties of carbon nanotubes and quantum dots using quantum chemistry semi-empirical methods.

International and national grants: awarded and applicated

[1] Grant Cooperacióninternacional para simulaciónde nanobio ACI-52, Ch$20 000,-, awarded in Janaury 2008. This grant has played a key rol in our international activities and collaboration. [2] PROYECTOS DE COOPERACION INTERUNIVERSITARIA UAM-SANTANDER con América Latina, application submitted, April 2009, led by E. Menendez y W. Orellana. Title: Estados electrónicos de grafenos, nanotubos de carbono, fulerenos y nanocristales con posibles dopantes Director: Jose Manuel Garcia de la Vega, Depto de Quimica Fisica Aplicada, Universidad Autonoma de Madrid. Participation: UAM, UChile, UNAB-Chile, U. Autonoma de Chihuahua-Mexico, UHabana-Cuba, 2009-2010 [3] Walter Orellana, Principal Investigator of the project: FONDECYT regular (2009- 2013) Theoretical investigation of nanoscale catalyst based on metallic nanoparticles and metallo-macrocyclic complexes [4] Daniel Laroze, Principal Investigator Proyecto Fondecyt Iniciacion, (2008-2010) NON- VARIATIONAL EFFECTS IN THE PARAMETRICALLY DRIVEN QUASIREVER- SIBLE SYSTEMS

[5] MAT2005-1872: Simulaciónde catalizadores: reactividad de superficies de TiO2 y SnO2 dopadas con C, N y Sb, interfase metal/soporte, y propiedades electrónicas de sistemas de tipo colorante/soporte. Director: Javier Fernandez Sanz; participation: U. de Sevilla- España,U. de Chile, 2008-2011 [6] Agencia Espñola de Cooperación Internacional (PCI/2006) Director: Norge Cruz peri- dodo: 2006

Participations in schools

[1] E. Menendez, Spring College on Water in Physics, Chemistry and Biology, Trieste, Italia (Apr. 2007) [2] C. Loyola, E. Valdebenito, J. Peralta, Minicurso de Nanomecanical, Santiago, Chile (Jun 2007) [3] C. Loyola, E. Valdebenito, J. Peralta, Minisimposio de F´ısicaTeórico-Experimental, F´ısicaNuclear, F´ısicade Sistemas Nanoscópicos y Nanomateriales, Santiago, Chile (Jul 2007) [4] C. Loyola, J. Peralta, Segundo Congreso Nacional de e-ciencia, Santiago, Chile (Sep. 2007 [5] C. Loyola, E. Valdebenito, J. Peralta, Escuela de Nanoestructuras, Valpara´ıso, Chile (Ene. 2008) [6] C. Loyola, E. Valdebenito, J. Peralta, Minicurso sobre Respuesta Mecanica de Mate- riales Desordenados, Santiago, Chile (Abr 2008) [7] G. Gutiérrez, Diplomado en biolog´ıacelular y molecular, Facultad de Ciencias, Univ. De Chile, Abril-Diciembre 2007 [8] W. Orellana, Diplomado en biolog´ıacelular y molecular, Facultad de Ciencias, Univ. De Chile, Abril- Diciembre 2007 [9] C. Loyola and J. Peralta, CCP5 “Methods in Molecular Simulation Summer School 2008” (http://www.ccp5.ac.uk/SSCCP5/main.html) 6-15 de july 2008 in Sheffield, United Kingdom.

VI. TRAINING OF STUDENTS, POST-GRADUATES AND YOUNG RESEARCHERS

This section consists mainly in the following table. Nevertheless, if there are special highlights that you consider should be mentioned in addition to the information required, please refer to Section III (RESEARCH RESULTS) making specific reference to the student or young researcher work.

Gender Type of Degree 2 Category in the University that gives the No. Name of student Thesis Title 1 Status Tutor's name (M/F) degree denomination Project degree

Computer simulation Resaerch Unit, 4th 1 Nicolas Viaux M 1 F-2008 Eduardo Menendez Titular University of Chile of materials year student Physics Introduction to Summer practice, 2 Varinia Bernales F 1 F-2008 Eduardo Menendez Titular University of Chile materials simulation Chemistry student Introduction to Summer practice, 3 Erick Nicolas Perez M 1 F-2008 Gonzalo Gutierrez Director University of Chile materials simulation Chemistry student Análisis mediante simulación molecular de los determinantes SAMUEL MORALES estructurales de la 4 M 1 Biochemist F-2008 Danilo González Nilo Titular Catholic University of Chile NAVARRO activación dependiente de volta je en canales de potasio de Arabi- dopsis thaliana Estudio de la interacción de las Jaime Henríquez cadenas laterales de Associate Roman RODRIGO URZUA los aminoáci- Bioinformatics 5 M 1 F-2009 University of Talca LEIVA dos que conforman el Engineer Eduardo Menendez oligopeptido RGD Titular Proupin sobre superﬁcies de TIO2 Caracterizaci´on del rol del residuo F380 en la VALERIA MARQUEZ Bioinformatics 6 F conductancia a 1 F-2008 Danilo González Nilo Titular University of Talca MIRANDA Engineer traves del canal de potasio hSlo

1 Undergraduate degree or professional title (1); Master or equivalent (2); Ph.D. or equivalent (3). 2 Finished (F-year) or In Progress (IP)

Estudio del perﬁl de CRISTELL NAVARRO Energıa Libre de iones Bioinformatics 7 F 1 F-2008 Danilo González Nilo Titular University of Talca NAVARRO de K+ en el canal Engineer de potasio TASK-2 Caracterización de la Danilo Gonzáalez Nilo Titular WALDO ACEVEDO interacción entre Bioinformatics 8 M 1 F-2009 University of Talca CASTILLO cluster de Aun y amino Engineer Jaime Henríquez Associate acidos azufrados Roman Estudio in- silico de la descarboxilación del Danilo Gonzáalez Nilo Titular XAVIERA LOPEZ oxaloacetato en Bioinformatics 9 F 1 F-2008 University of Talca CORTES fosfoenolpiruvato Engineer Jaime Henríquez Associate carboxiquinasa de Roman Saccharomyces cerevisiae Structural and Electrostatic properties in the permeation pat- ARIELA VERGARA Bioinformatics 10 F hway of Shaker 1 F-2008 Danilo González Nilo Titular University of Talca JAQUE Engineer potassium channel and the mutants P475D and P475Q Claudia Loyola PhD student Molecular dynamics of Research Unit, 4th 11 Diego Cohen M 1 F-2009 University of Chile cluster collisions year Physics student G. Gutierrez Director Visualization for the Research Unit, 4th Joaquin Peralta PhD student 12 Yasmin Navarrete F 1 F-2009 University of Chile LPMD code year Physics student G. Gutierrez Director Visualization for the Research Unit, 3rd Joaquin Peralta PhD student 13 Pablo Ravelo M 1 F-2009 University of Chile LPMD code year Physics student G. Gutierrez Director Claudia Loyola PhD student Molecular dynamics of Research Unit, 3rd 14 Rodrigo deNegri M 1 F-2009 University of Chile hypervelocity impact year Physics student G. Gutierrez Director 4th year chemistry 15 Daniela Riuz F Ab initio clculations 1 IP E. Menendez Titular University of Chile un dergraduate Elastic constants of training, 2nd year 16 Ricardo Osorio Pulgar M 1 F-2010 E. Menendez Titular University of Chile hydroxiapatite, student of physics Interaction of the amino acids of the Engineer in 17 Jorge Mansilla Sierra M RGD sequence with 1 F-2010 E. Menendez Titular University of Talca Bioinformatics titanium dioxide surfaces Introduction to Research unit, 3rd 18 Mauricio Franco Cisterna M atomistic materials 1 year student of F-2010 E. Menendez Titular University of Chile simulation Physics

Research unit, 4rd 19 Nicolas Amigo M Hypervelocity impact 1 year student of F-2009 Gonzalo Gutiérrez Director University of Chile Physics Mechanical properties Research unit, 3rd of proteins by 20 Diego Contreras M 1 year student of F-2010 Gonzalo Gutiérrez Director University of Chile computer simulation Physics techniques Bouncing of a cube under gravity: Research unit, 3rd 21 Felipe Gonzalez Wassaf M molecular dynamics 1 year student of F-2010 Gonzalo Gutiérrez Director University of Chile simula- Physics tion Impact of nanosphere: Research unit, 3rd 22 Camila Rioseco F molecular dynamics 1 year student of F-2010 Gonzalo Gutiérrez Director University of Chile simulation Physics Impact of nanosphere: Research unit, 3rd 23 José Rojas M molecular dynamics 1 year student of F-2010 Gonzalo Gutiérrez Director University of Chile simulation Physics 24 Eduardo Valdebenito M 2 Master in Science IP Gonzalo Gutiérrez Director University of Chile 25 Fernando Cuturrufo M 2 Master in Physics F-2009 Gonzalo Gutiérrez Director University of La Serena PROPIEDADES ESTÁTICAS Y DINÁMICAS DE Patricio Vargas NANOESTRUCTURAS Universidad Federico Santa 23 Omar Suarez M 2 Master in Physics MAGNÉTICAS Maria INTERACTUANTES David Larozze Associate CON GEOMETRÍA CILÍNDRICA Jorge Cancino Magister en 24 Marcelo Tuesta M 2 Universidad Mayor Educación Física D. Laroze Associate Physical properties of new materials by 25 Joaquin Peralta M 3 Phd in Physics F-2010 Gonzalo Gutiérrez Director University of Chile means of computer simulation methods Study at atomic level of nanostructured 26 Claudia Loyola F materials by means of 3 Phd in Physics F-2010 Gonzalo Gutiérrez Director University of Chile computer simulation methods Materiales en condiciones extremas: 27 Felipe González M 3 Phd in Physics IP Gonzalo Gutiérrez Director University of Chile aplicaciones al estudio del interior de planetas

solares y extrasolares Catalytic properties of metallomacrocycles attached to carbon 28 Igor Ruiz-Tagle M 3 PhD in Chemistry IP Walter Orellana Associate Universidad Andres Bello nanostructures: A theoretical study 29 Paula Escobar F 3 Phd in Physics IP Eduardo Menendez Titular University of Chile Insights into role of the induced conformational DANIEL AGUAYO changes in the PhD Program of 30 M 3 IP Danilo González Nilo Titular University of Talca VILLEGAS VP1/VP2/RNA Applied Science complexes on the rotavirus SA11 RNA replication. Structural, molecular and phenotype characterization of vol- Danilo González Nilo Titular tage, pH and abiotic WENDY GONZALEZ PhD Program of 31 F stress regulation in 3 F-2009 University of Talca DIAZ Biotechnology KAT1 and SKOR Simon Ruiz channels of Arabidopsis thaliana Implementation of chemical conditions for HEGALY MENDOZA PhD Program of 32 F protein crystalliza- 3 IP Raul Cachau Associated University of Talca VILCHES Applied Science tion using chips based on semiconductors Models and molecular dynamic simulations of PhD Program of 33 JULIO CABALLERO M 3 IP Danilo González Nilo Titular University of Talca dendrimer-related Applied Science systems Theoretical studies on Stella Ordóñez the dynamical Dr. in Materials 34 Laura Milena Perez F 3 IP University of Santiago behaviours of magnetic Science Associate D. Laroze system

Spatiotemporal Iván Schmidt Universidad Federico Santa 35 Pablo Diaz M dynamics of Bose- 3 Dr. in Physics IP David Larozze Associate Maria Fermi mixtures

PAMAM-QDs based 36 DANIELA GERALDO F 4 Postodoctoral F-2009 Danilo González Nilo Titular University of Talca nanocomposite for

ﬂuorescent labelling of early stage cancer STUDY OF BIOLOGICAL 37 PABLO ENCINA M SYSTEMS UNDER 4 Postodoctoral IP Gonzalo Gutiérrez Director University of Chile THE EFECT OF SHOCK WAVES STUDY OF MELTING OF SOLIDS USING ATOMISTIC 38 SERGIO DAVIS M 4 Postodoctoral IP Gonzalo Gutiérrez Director University of Chile COMPUTER SIMULATION TECHNIQUES MECHANICAL AND COOPERATIVE PROPERTIES OF 39 GERMAN MIÑO M 4 Postdoctoral IP Gonzalo Gutiérrez Director University of Chile DIMERIC PROTEINS. A COMPUTATIONAL SIMULATION STUDY Antonio Galdamez training in ab initio 40 Fernanda Lopez F 3 PhD in chemistry IP Titular University of Chile calculations Eduardo Menendez

Note: Please consider all the students registered in previous progress reports.

13 VII. PUBLICATIONS

Papers Abril 2007-2010

[1] Magnetostatic interactions between two magnetic wires, R. Picin, D. Laroze, M. Knobel, P. Vargas, M. Vazquez, Europhysics Letters 78, 67004 (2007). [2] Thermal Convection in a Rotating Binary Maxwell liquid Mixture, D. Laroze, J. Mar- tinez Mardones, J. Bragard, European Physical Journal S.T. 146, 291 (2007). [3] A detailed analysis of dipolar interactions in arrays of bi-stable magnetic nanowires, D. Laroze, J. Escrig, P. Landeros, D. Altbir, M. Vazquez, P. Vargas, Nanotechnology 18, 415708 (2007) [4] On the probably transition of a quantum dot in a time dependent magnetic field, D. Laroze, R. Rivera, Revista Mexicana de F´ısica S 53, 112 (2007). [5] Realistic rotating convection in a DNA suspension, D. Laroze, J. MartinezMardones, J. Bragard, C. PerezGarcia Physica A 385, 433 (2007). [6] Dissection of the components for PIP2 activation and thermosensation in TRP channels, S. Brauchi, G. Orta, C. Mascayano, Salazar M, N. Raddatz, H. Urbina, E. Ro- senmann, F. Gonzalez-Nilo, R. Latorre, Proc Natl Acad Sci U S A 104, 10246 (2007). [7] In-silico nanobio-design. A new frontier in computational biology, R.E. Cachau, FD Gonzalez-Nilo, O.N. Ventura, M.J. Fritts, Curr Top Med Chem. 7, 1537 (2007). [8] Molecular in situ studies of atmospheric corrosion, C. Leygraf, J. Hedberg, P. Qiu, H. Gil, J. Henriquez, and C. M. Johnson, Corrosion 63, 715 (2007). [9] Classical spin dynamics of four interacting magnetic particles on a ring, D. Laroze, L. M. Perez, Physica B 403, 473 (2008). [10] Dynamics of two interacting dipoles, D. Laroze, P. Vargas, C. Cortes, G. Gutierrez, Journal of Magnetism and Magnetic Materials 320, 1440 (2008). [11] Intrinsic electrostatic potential in the BK channel pore: role in determining single channel conductance and block, I. Carvacho, W. Gonzalez, Y.P. Torres, S. Brauchi, O. Al- varez, F.D. Gonzalez-Nilo, R. Latorre, J. Gen. Physiol. 131, 147 (2008) [12] 2D Autocorrelation, CoMFA, and CoMSIA modeling of protein tyrosine kinases´ınhibi- tion by substituted pyrido[2,3-d]pyrimidine derivatives, J. Caballero, M. Fernández, M. Saavedra, F.D. González-Nilo, Bioorg. Med. Chem. 16, 810 (2008). [13] A CoMSIA study on the adenosine kinase inhibition of pyrrolo[2,3-d]pyrimidine nucleo- side analogues, J. Caballero, M. Fernández, F.D. Gonzalez-Nilo, Bioorg. Med. Chem. 16, 5103 (2008). [14] Localized states beyond asymptotic parametrically driven amplitude equation, M. G. Clerc, S. Coulibaly and D. Laroze, Physical Review E 77, 056209 (2008). [15] Initial Atmospheric Corrosion of Zinc exposed to Formic acid, Investigated by in-situ Vibrational Sum Frequency Spectroscopy and Density Functional Theory calculations, J. Hedberg, J. Henriquez, S. Baldelli, M. Johnson, C. Leygraf, Journal of Physical Chemistry C, 113, 2088-2095 (2008). [16] Strength of polycrystalline coarse-grained platinum to 330 Gpa and of nanocrystalline platinum up tu 70 Gpa from high-pressure x-ray diffraction data, A. K. Singh, H-P. Liermann,Y. Akayama, S. K.Saxena, and E. Menéndez-Proupin, Journal of Applied Physics 103, 063524 (2008). [17] Study of the interaction between progesterone and beta-cyclodextrin by electrochemical techniques and steered molecular dynamics. Caballero J, Zamora C, Aguayo D, Yañez C, González-Nilo FD. , J Phys Chem B. 112(33):10194-201. Aug 21 (2008). Epub 2008 Jul 30.(ISI:4,086) [18] Stability and bonding properties of finite single-walled carbon nanotubes adsorbed on Si(001), W. Orellana, Applied Physics Letters 92, 093109 (2008). [19] Iron silicide wires patterned by Bi nanolines on the H/Si(001) surface: Spin-density functional calculations, R.H. Miwa, W. Orellana and G.P. Srivastava, Physical Review B 78, 115310 (2008) [20] Noncollinear magnetism in the high-pressure hcp phase of iron, Raquel Lizárraga, Lars Nordström,Olle Eriksson, and John Wills, Phys. Rev. B 78, 064410 (2008) [21] Dynamics of a rotating particle under a time-dependent potential: exact quantum solu- tion from the classical action, D. Laroze, G. Gutiérrez, R. Rivera and J. Yáñez, Physica Scripta 78, 015009 (2008). [22] Structural and vibrational properties of amorphous GeO2: a molecular dynamics study, J. Peralta, G. Gutierrez and J. Rogan, J. Phys.: Conden. Matter 20, 145215 (2008). [23] Distinct roles of the last transmembrane domain in controlling Arabidopsis K+ channel activity. Gajdanowicz P, Garcia-Mata C, Gonzalez W, Morales-Navarro SE, Sharma T, Gonzalez-Nilo FD, Gutowicz J, Mueller-Roeber B, Blatt MR, Dreyer I. New Phytol. 182(2):380-91 (2009). Epub 2009 Jan 14(ISI:5,249) [24] Shared and Group-Specific Features of the Rotavirus RNA Polymerase Reveal Potential Determinants of Gene Reassortment Restriction. S. M. McDonald, D. Aguayo, F. D. Gonzalez-Nilo, and J. T. Patton, Journal of Virology, , p. 000 Vol. 83, No. 12. 0022, June 2009 (ISI:5,332) [25] Docking and quantitative structure-activity relationship studies for sulfonyl hydrazides as inhibitors of cytosolic human branched-chain amino acid aminotransferase. Caba- llero J, Vergara-Jaque A, FernándezM, Coll D. Mol Divers. Apr 7(2009)(ISI: 2,708) [26] A computational ONIOM model for the description of the H-bond interactions between NU2058 analogues and CDK2 active site Alzate-Morales, JH; Caballero, J; Gonzalez- Nilo, FD; Contreras, R., Chemical Physics Letters, 479, 149-155, (2009) [27] Saldias C, Gargallo L, Sandoval C, Leiva A, Radic D, Caballero, Saavedra M, Gonzalez- Nilo FD, POLYMER 50 (13), 2926-2932 (2009) [28] Configurational temperature for interacting anisotropic magnetic particles, P. Diaz and D. Laroze, International Journal of Bifurcation and Chaos 19, 3485-3498 (2009). [29] Ab initio molecular dynamics study of amorphous CdTeOx alloys: Structural properties, E. Menéndez-Proupin, P. Giannozzi, J. Peralta, and G. Gutiérrez,Phys. Rev. B 79, 014205 (2009). [30] Reaction and incorporation of H2 molecules inside single-walled carbon nanotubes through multivacancy defect, W. Orellana, Physical Review B 80, 075421 (2009). [31] Amplitude equation for stationary convection in a rotating binary ferrofluid, D. La- roze, J. Martinez-Mardones, L. M. Perez, Y. Rameshwar , International Journal of Bifurcation and Chaos, Vol. 19, No. 8 (2009) 2755-2764. [32] Localized states and non-variational IsingBloch transition of a parametrically driven easy-plane ferromagnetic wire, Marcel G. Clerc , Saliya Coulibaly, and David Laroze, Physica D 239, 72-86 (2009). [33] Nonvariational IsingBloch transition in parametrically driven systems, M. G. Clerc, S. Coubaly, and D. Laroze, International Journal of Bifurcation and Chaos, Vol. 19, No. 8 (2009) 2717-2726. [34] Investigation of interface properties of Ni/Cu multilayers by high kinetic energy photoelectron spectroscopy, Sari Granroth, Ronny Knut, Moreno Marcellini, Gabriella An- dersson, Svante Svensson, Olof Karis, Mihaela Gorgoi, Franz Schäfers,Walter Braun, Wolfgang Eberhardt, Weine Olovsson, Erik Holmström,Nils Martensson, PHYSICAL REVIEW B 80, 094104 (2009) [35] Modularity density of network community divisions, Erik Holmström, Nicolas Bock, Johan Brännlund Physica D 238 (2009) 1161-1167 [36] Ab initio method for locating characteristic potential-energy minima of liquids, E. Holmström,N.Bock, Travis B. Peery, R. Lizárraga, G. De Lorenzi-Venneri, Eric D. Chisolm, and Duane C. Wallace PHYSICAL REVIEW E 80, 051111 (2009). [37] First Principle Calculations of Core-Level Binding Energy and Auger kinetic Energy Shifts in Metallic Solids, Weine Olovsson, Tobias Marten, Erik Holmstrom, Borje Johansson, Igor A. Abrikosov, Journal of Electron Spectroscopy and Related Phenome- na 178-179, Trends in X-ray Photoelectron Spectroscopy of solids (theory, techniques and applications), 88-99 (2009). [38] Quantitative local environment characterization in amorphous oxides, A. Amézaga, E. Holmström,R. Lizárraga, E. Menéndez-Proupin, P. Bartolo-Pérez, and P. Giannozzi, Phys. Rev. B 81, 014210 (2010). [39] Core-level shift analysis of amorphous CdTeOx materials, R. Lizárraga, E. Holmström, A. Amézaga, N. Bock , T. Peery, E. Menéndez-Proupin, and P. Giannozzi, J. Mater. Sci. 45, 5071-5076 (2010). [40] Iron porphyrins attached to single-walled carbon nanotubes: Electronic and dynamical properties from ab initio calculations, I. Ruiz Tagle, W. Orellana, Physical Review B 82, 115406 (2010). [41] Characterization of spin-state tuning in thermally annealed semiconductor quantum dot, E. Margapoti, Fabrizio M. Alves, V. Lopez-Richard, C. Destefani, G. E. Marques, E. Menéndez-Proupin, Fanyao Qu, S. Mahapatra, K. Brunner, and C. Bougerol , Phys. Rev. B 82, 205318 (2010). [42] Approximate quantum mechanical method for describing excitations and related properties of finite single-walled carbon nanotubes, A. L. Montero , M. E. Fuentes, E. Menéndez-Proupin, W. Orellana, C. F. Bunge, L. A. Montero, and J. M. Garc´ıade la Vega, Phys. Rev. B 81, 235409 (2010). [43] Las Palmeras Molecular Dynamics: A flexible and modular molecylar dynamics code, S. Davis, C. Loyola, F. González,and J. Peralta, Computational Physics Communication 181 2126-2139 (2010). [44] Onset of failure in argon by the effect of a shockwave: A molecular dynamics study, Claudia Loyola, Sergio Davis, Joaqu´ınPeralta, and Gonzalo Gutiérrez, Computational Materials Science 49, 582-587 (2010). [45] Computer simulation study of amorphous compounds: structural and vibrational properties, G. Gutiérrez,E. Menéndez-Proupin, C. Loyola, J. Peralta, and S. Davis, J. Mater. Sci. 45, 5124-5134 (2010).

[46] Atomistic study of vibrational properties of gamma-Al2O3, C. Loyola, E. Menéndez- Proupin, and G. Gutiérrez, J. Mater. Sci. 45, 5094-5100, (2010). [47] Efficient Spin Injection Through Exchange Coupling at Organic Semiconduc- tor/Ferromagnet Heterojunctions, Yiqiang Zhan, Erik Holmström,Raquel Lizárraga, Olle Eriksson, Xianjie Liu, Fenghong Li, Elin Carlegrim, Sven Stafström, Mats Fahl- man, Advanced Materials 22, 1626-1630 (2010) [48] Theoretical studies of the incommensurate magnetic structure of a heavy fermion system: CeRhIn5, TorbjörnBjörkman, Raquel Lizárraga, Fredrik Bultmark, Olle Eriksson, John M. Wills, Anders Bergman, Per H. Andersson, and Lars Nordström, Phys. Rev. B 81, 094433 (2010). [49] Computational Study of the Interactions between Guanine Derivatives and Cyclin- Dependent Kinase 2 (CDK2) by CoMFA and QM/MM, Julio Caballero, Jans Alzate, Journal Of Chemical Information And Modeling 50, 110-122 (2010) [50] Structural and dynamical properties of the Cu46Zr54 alloy in crystalline, amorphous and liquid state: a molecular dynamic study, C. Valencia-Balv´ın,C. Loyola, J. Osorio and G. Gutiérrez. Physica B 405, 4970-4977 (2010). [51] Distributed Structures Underlie Gating Differences between the K-in Channel KAT1 and the K-out Channel SKOR, Riedelsberger J, Sharma T, Gonzalez W, Gajdanowicz P, Morales-Navarro SE, Garcia-Mata C, Mueller-Roeber B, Gonzalez-Nilo FD, Blatt MR, Dreyer I, MOLECULAR PLANT 3 (1), 236-245 (2010) [52] Gating of a pH-Sensitive K-2P Potassium Channel by an Electrostatic Effect of Basic Sensor Residues on the Selectivity Filter, Zuniga L, Marquez V, Gonzalez-Nilo FD, Chipot C, Cid LP, Sepulveda FV, Niemeyer MI, PLOS ONE 6 (1) Article Number: e16141 (2011). [53] Nanoinformatics: an emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology, Gonzalez-Nilo F, Perez- Acle T, Guinez-Molinos S, Geraldo DA, Sandoval C, Yevenes A, Santos LS, Laurie VF, Mendoza H, Cachau RE, BIOLOGICAL RESEARCH 44 (1), 43-51 (2011) [54] Supramolecular complexes of quantum dots and a polyamidoamine (PAMAM)-folate derivative for molecular imaging of cancer cells, Geraldo DA, Duran-Lara EF, Aguayo D, Cachau RE, Tapia J, Esparza R, Yacaman MJ, Gonzalez-Nilo FD, Santos LS, ANALYTICAL AND BIOANALYTICAL CHEMISTRY 400 (2), 483-492 (2011) [55] Nitrogen/Gold Codoping of TiO (101) Anatase Surface. A Theoretical Study Based on DFT Calculations Yanaris Ortega, Norge Cruz Hernández, Eduardo Menéndez- Proupin, JesúsGraciani and Javier Fdez. Sanz, accepted to Physical Chemistry Che- mical Physics (PCCP). [56] Computer simulation of elastic constants of hydroxyapatite and fluorapatite, E. Menéndez-Proupin, S. Cervantes-Rodriguez, R. Osorio-Pulgar, M. Franco-Cisterna, H. Camacho-Montes, and M. E. Fuentes, accepted to Journal of the Mechanical Behavior of Biomedical Materials.

Non-ISI papers

[57] Convective instability of viscoelastic ferrofluid, D. Laroze, J. Martinez-Mardones , AIP Conference Proceeding 913, 9 (2007). [58] Dynamical behaviour of two Interacting Dipoles, C. Cortés, P. Vargas, G.Gutiérrez, and D. Laroze Journal of Physics: Conference Series 134, 012016 (2008).

Papers, submitted

[59] Structural transformation of amorphous Al2O3 under pressure: a molecular dynamics study , G.Guti´errez, submitted PRB. [60] Structural, elastic, vibrational, and electronic properties of amorphous Al2O3 from ab- initio calculations, S. Davis and G. Guti´errez,submitted to J. Chemical Physics.

[61] Thermal stability and dynamical properties of Ti3SiC2 (0001) at high temperatures: First-principles calculations, Walter Orellana and Gonzalo Guti´errez,submitted to Acta Materialia. VIII. DISSEMINATION AND KNOWLEDGE TRANSFER AC- TIVITIES

Schools, workshops, courses, and lectures organized by the Anillo

[1] Workshop de SimulaciónMolecular: Energ´ıaLibre. Profesor invitado Dr. Christophe Chipot, CNRS/Nancy-Francia. Con máde 45 participantes, se discutiósobre métodos y herramientas computacionales avanzadas para la evaluaciónde energ´ıalibre en sistemas complejos. Talca, 19-21 Nov. 2007. [2] VI Encuentro de Modelos F´ısicos y Matemáticos en Ingenier´ıa EMFIMIN 2007. Noviembre 15-16, 2007, Santiago, Chile. [3] Curso de postgrado F´ısica Cuántica Aplicada a la Ciencia de Materiales. Facultad de Ciencias, Universidad de Chile, impartido por G. Gutiérrez,E. Menéndezy W. Orellana. Asistieron 10 alumnos, cuatro estudiantes del proyecto. March-July 2007. [4] Latinamerican School in Computational Materials Science (see http://www.gnm.cl/school/ ). This activity, organized by the Anillo researchers E. Menendez and W. Orellana with S. Scandolo (ICTP), P. Gianozzi (Democritos/U. Udine) and S. Cozzini (Democritos/Sissa). It was a joint effort of our Anillo Project, two chilean universities (U. de Chile and UNAB), the Italian National Simulation Center, and the UNESCO International Centre for Theoretical Physics of Trieste. The activity consisted on a course in High Performance Computing, and advanced workshop, and a tutorial course on the ab initio simulation package Quantum-ESPRESSO. In total, the activity lasted two weeks, and received 54 student participants, 30 from Chile and 24 from Argentina, Brazil, Peru, Colombia, Mexico, and Uruguay. Also attended 15 foreign and 6 national advanced scientists that acted as speakers and professors. This activity marked an important step in terms of international contacts and recognition for our group as a regional force in the topic of computational materials science. [5] Advanced Course on Free Energy Calculations: Theory and Practice Coordinator, Da- nilo Gonzalez. This course was given in the CBSM of the Universidad de Talca, Talca. The course had 45 pedagogic hours, during 5 days period, from December 15 to 19, 2008. This course was co-financed by the PhD program in Applied Sciences of the UTalca, by the European Community FP7 ACTION-GRID project (local coordinator: Danilo Gonzalez) and by the our Project Anillo ACT/24. This event had the participation of 25 PhD students from the Applied Science and Biotechnology PhD programs of the Universidad de Talca. All the integrants of the Anillo participated. Also professors and students from Universidad de Santiago (USACH), Universidad de Chile, Universidad de Valpara´ıso,Universidad Austral de Valdivia and from Pontificia Universidad Católicade Chile were present. During the course, it was discussed advanced methods of free energy calculation across a reaction coordinate, utilizing the ABF method (Adaptive Biasing Forces). It was also done advanced tutorials of simulations of molecular dynamics and of molecular visualization using the VMD program. [6] Physics of proteins. Course given by Dr. C. Camacho, University of Pittsburgh, Physics of Proteins from 11-14 August 2008, 4.5 hrs., 18 people (PhD student, undergraduate and researchers) attended. [7] Tutorial course of Quantum-ESPRESSO delivered by E. Menendez, was taught by invitation of the University of Chihuahua, in Mexico. This course had a duration of five days (25 hours) and was attended by ten scientists and students of several research institutions of the state of Chihuahua. November 2008. [8] Introductory course on structural bioinformatics and drug design, given by J. Alzate, National University of Rio Cuarto, Rio Cuarto, Argentina. November 24-26, 2008. [9] Course Shock Waves, Second Semester, July-Dec. 2008. Course was given at Fa- cultad de ciencias, Universidad de Chile. Coordinator Gonzalo Gutierrez, Lectu- rers: L. Moraga, G. Gutierrez, M. Brañes. (ver http://fisica.ciencias.uchile.cl/ gonzalo/?n=Docencia.2008OndChq) [10] Métodos simplificados para cálculos de estructura electrónica, Profesor Jorge Kohanoff, de la Queens University Belfast, en el laboratorio de GNM los d´ıas 18, 20 y 21 de Agosto desde las 14:00 hasta las 17:00 hrs. El curso incluyóun trabajo prácticocon un programa basado en Tight-binding Molecular Dynamics. Attende by 12 students. [11] Simposio Y - Computational Modeling and Data Driven Materials Discovery, ICAM09 (11th International Conference on Advanced Materials), Rio de Janeiro, 20-25 de Sep- tiembre 2009: Co-chair G. Gutiérrez,GNM. [12] Taller de ModelaciónMultif´ısica mediante Elementos Finitos, 18 dic 2009, Sala 1, Auditórium Albert Einstein Departamento de F´ısicade la Facultad de Ciencias (Las Palmeras 3425 NuñoaSantiago)˜ (56) (2) 9787441 Grupo de Nanomateriales, U. de Chile. [13] NanoTaller Python, 12-13 Jan 2009. Basic notion about Python language, given at Facultad de Ciencias by S. Davis, PhD student at KTH, Sweden, and member of GNM. More than 20 student attended it. [14] First International Conference on Bioinformatics, organized by the Ibero-American Society for Bioinformatics (SoIBio) (2010). [15] Escuela de SimulaciónComputacional de dinámica molecular clásica: Las Palmeras MD, 4-8 de Enero de 2010, Facultad de Ciencias, Universidad de Chile, Santiago. More than 20 sudent attended. See http://www.lpmd.cl/school/ [16] In addition, we have supported the Symposium of the Chilean Physical Society and partially supported the attendance of more than 20 undergraduate student form U. Chile to that event. Technical Colloquia

[11] D. Laroze, Localizaciónen sistemas magnéticosextendidos, Departamento de F´ısica, Universidad de la Frontera, Temuco, Chile (Nov. 2007). [12] D.Laroze, Termodinámica y Dinámicaen sistemas magnéticos, Universidad de Tara- pacá, Arica, Chile (Mar. 2008). [13] E. Menendez, Simulaciónde la estructura de vidrios de CdTeOx, Facultad de Ciencias F´ısicas y Matemáticas, Universidad de Chile, Santiago, Chile (Mar. 2008); also at Facultad de Ciencias, U. de Chile (Abr. 2008). [14] G. Gutiérrez, Ab-initio calculations in materials, CESMEC, FIU, Miami, (Ene. 2007) [15] G. Gutiérrez,Equilibrio termico en sistemas magneticos, Facultad de Ciencias Fisicas y Matematicas, Universidad de Chile, Santiago, Chile (Jun. 2007) [16] G. Gutiérrez,Simulacióncomputacional de materiales, Departamento de F´ısica,U. de Concepción(Abril 2008). [17] G. Gutierrez, Seminars at: Departamento de F´ısica,Universidad de Concepción, April 08; Taller Nanociencia, VRID, UChile, April 08; Departamento de Qu´ımica, Facultad de Ciencias, Nov 08; Departamento de F´ısica,F. Ciencias F´ısicasy Matemáticas, U. de Chile, Dic.08. [18] E. Menendez: Seminars at Universidad de Chile, Universidad de Valencia, Spain, Uni- versidad de Sevilla, Spain. [19] D. Laroze, Seminars at Instituto de Alta Investigación,Arica, Chile; Anillo de Fisica No Lineal , Santiago, Chile. [20] G.Gutiérrez,Charla Simulacióncomputacional de materiales, Ecuela de Dinámica Mo- lecular, LPMD, Facultad de Ciencias, U. de Chile, Ene. 2010.

Talk to the public at large, high schools, etc.

[21] Charla de difusión Auditorio Abate Molina a Estudiantes de Enseñanza media de la VII Región. Esta actividad permitióexplicar, a mas de 600 alumnos seleccionados de diversos liceos de la VII región, las actividades desarrolladas en nuestro Anillo Cient´ıfico. [22] E. Menéndez, Charla “Puntos cuánticos”, Colegio Latino-Cordillera (9/10/2007), en el marco de la actividad 1000 cient´ıficos, 1000 Aulas, del programa EXPLORA. [23] Actividad de puertas abiertas. Facultad de Ciencias. Universidad de Chile. Presentación de stand por parte de Anillo ACT-24, Oct. 2007. [24] G. Gutiérrez,Charla Nanotecnolog´ıa,dictada en: Inauguracióndel Ciclo de charlas cient´ıficaspara estudiantes de Enseñanzamedia, Direcciónde Extensión,Facultad de Ciencias, U de Chile, 16/05/2007; Liceo Manuel de Salas, Julio 2007; Scuola Italiana de Santiago Agosto 2007; Instituto Nacional Octubre 2007. [25] G. Gutiérrez, Charla Transporte de calor en sistemas magnéticos: un ejemplo de “spintrónica”, II Escuela de Invierno para la divulgación de la Robótica, Nanotec- nolog´ıay Neurociencia, UTFSM, Valpara´ıso, Agosto 2008. [26] G.Gutiérrez,Charla Nanotecnolog´ıa, Colegio Jungenland Schule, Talagante, Nov. 2008. [27] W. Orellana, Nanomateriales y Nanotecnolog´ıa, Olimpiada Chilena de F´ısica, Univer- sidad AndrésBello, (October 2008). [28] W. Orellana, Nanomateriales y Nanotecnolog´ıa, Colegio P´ıaMarta, EstaciónCentral, (August 2008). [29] D. Laroze, Estudios de Doctorado en la Universidad de Tarapaca, SOBOFI, La Paz, Bolivia (Nov. 2008). [30] G.Gutiérrez,Charla El juego de los átomos:materiales avanzados, Charla inaugural exposiciónExplora-Conicyt, Museo de Historia Natural, Quinta Normal, Julio 2009. [31] G.Gutiérrez,Charla Necesidades energéticas y nanotecnolog´ıa, Instituto Rafael Arizt´ıa, Quillota, Oct. 2009. [32] G.Gutiérrez,Charla Necesidades energéticas y nanotecnolog´ıa, Semana de la Ciencia Colegio San Ignacio El Bosque, Nov. 2009.

Press

[29] G. Gutiérrez,Radio interview, Radio Universidad de Chile, programa Milenio, 03. Ene.2007. [30] G. Gutiérrez,Radio interview, Radio Universidad de Chile, programa Semáforo Cul- tural, 9 Abril 2007, a G. Gutiérrez. Connection with the productive sector This year we have been able to develop several initiative in order to establish real links with the productive sector of our country. We are very happy with this new branch of our Anillo, that allows us to do research but also to contribute to the development of our industries as well as to create new possibilities for our student and associates. This initiative is in progress and both the group of Universidad de Talca, CBSM (which has been particularly aggressive in this respect) and the Group of NanoMaterials at Universidad de Chile are working hard to develop and consolidate the connection to the productive sector. 1. ADJUDICATION OF FONDEF TIC EDU FOR EDUCATION: in the education sector, our group, together with the Bioinformatics group (CBUC) from the Universidad Catolica, directed by Dr. Tomas Perez-Acle, got the adjudication of the project titled: Collaborative Learning System Based on Grid Infrastructure (SACGRID): Applications in Biological Sciences and Biotechnology. This project will be financed by the tender of Program Technology of Information and Effective Communications for Education (TIC EDU) from the FONDEF program of CONICYT. SACGRID is a 36 months project, with a budget of Ch$ 287.900.000 (US$ 480.000). The working team is formed by inves- tigators of the Foundation Science for the Life (David Holmes and Pablo Rosenblatt), the Universidad de Talca (Danilo Gonzalez and Sergio Guiñez) and the Universidad Catolica (Tomas Perez Acle and Jorge Manzi). Microsoft Chile, HP Chile and Coffee Business participate as strategic partners of SACGRID. 2. CONSULTING IN THE PROJECT Thermophysical properties of the tires used in mining trucks. We have been working in the modeling of truck tires together the company IICLtda (http://www.iicltda.cl/). This company have close links to the copper mining industry, and work in several projects with them. We (Prof. G. Gutierrez and L. Moraga from GNM and a Mathematical Engineer’s student ) developed a model based on the Thermodynamic theory of continuous media. The contract with IICLtda was about US$11000.- for four months. The work also included the advice in the experimental side. 3. APPLICATION TO BASAL PROJECT. A multidisciplinary group, leaded by researchers from the Universidad de Talca, and including people from CChen (State Nuclear Energy Agency), U. de Chile (Group of NanoMaterials) among others, , and private companies, got together to postulate to the Basal project, for a total budget of 6.000 million pesos (US$ 10.000.000), for a 5 years period. This group was led by Dr. Danilo Gonzalez and considered the development of three areas: pulse power physics, nanobiology and precision agriculture. Each one of these areas was coordinated in investigation in the areas of food, mining and medicine. This project was provided with the support of the Institute Fraunhoffer-Germany, NCI-USA, CODELCO, ECOMETALES, Bio- Frutales S.A, SUN Microsystem, among other companies. This project was presented in January, 2008, shortlisted in February and had a negative response on March 8. 4. ADJUDICATION OF FONDEF NANOFOOD: the CBSM together with the Faculty of Agronomy and the Instituto de Qu´ımicaof the Universidad de Talca, postulated a FONDEF project titled: Nanobiology applied to the food industry: Quality assurance and improved commercial value. For this project, we had the support of Fraunhoffer Institute-Germany, BioFrutales SA and SUN Microsystem. This project has as objective to implement a system based on nanoparticles for the specific extraction of non-desired molecules (e.g.: pesticides) in liquid food, such as wine, oils and fruits juices. IX. LESSONS LEARNED

The following section can be used in case of available information related to the possible diﬃculties, inconveniences or similar issues in the management of the project within the host institution, between CONICYT and the host institution, institution and researchers or any other combination of participants and activities involved. The idea is to resolve these issues on behalf of better practices in the current and future handling of these initiatives. Information provided in this section must be concise, stating all variables involved and outco- mes. Do not extend further than 2 pages. Indicate the need of conﬁdentiality when required.

The Anillo project allows us to develop research in a medium scale, that would be impossible with other kind of grant, like Fondecyt. Even summing our individual Fondecyt grant, we could not afford activities like those international schools we organized, neither the invitation to researcher and graduate student to spent some time with us, nor the installation of the high performance computer facility we did. These kind of activities are vital in order to enhance the vision and experience to student and researcher, particularly in a country like Chile, which is far away from the scientific capitals. Thus, we consider quite important to continue which this initiative, that give the opportunity to small group to do research with optimal conditions. For group like us, with two or three researcher in each universities, this grant are ideal: fondecyt is only individual, and that large grant like Financiamiento Basal or Fondap are to big, that you need to include to many different topics. We expect to continue tis initiative, in order to give sustaintability of Anillos like ours, that have consolidate in one research team different groups, like one in Santiago and the other in Talca.

X. INDICATORS

The following table corresponds to a selection of general and specific indicators that may or may not apply to the scope of your project. If you require or would like to define indicators particular to your activities and results, please include them at the end of this table. This program is aware that quantitative indicators do not cover most of the actual impact of your activities.

Please add up here all outputs resulting from the three-year period.

N° of Main Researchers 3 N° of Associated Researchers 3 F =0 General Gender (%) of the main researchers M =100 F =0 Gender (%) of the associated researchers M =100 Nº of ISI publications 56 Nº of non- ISI publications 2 Percentage of publications Co-authored with 70% Scientific researchers of the Project production Average impact index of ISI publications 3 Average number of citations per article up to this date 5 N° of international presentations/conferences 47 N° of national presentations/conferences 57 N° of patent applications 0 N° of patents granted 0 N° of licenses and/or material transfer agreements 2 Commercial or N° of Spin-offs other 1 Percentage of the annual funding of the project production 1% (only if applies) received from companies Annual sales volume of the companies involved ? N° of employees of the companies involved 10 Industrial sector of the companies involved Mining

Number of undergraduate students 23 Female (%) of undergraduate students 35% Number of Master’s students 4 Female (%)of Master’s students 0 Number of Ph.D. students 11 Female (%)of Ph.D. students 45% Human Number of postdocs participating in the project 4 resources training Female (%)of postdocs 25% Number of undergraduate theses finished 8 Number of graduate theses finished (Master) 3 Number of graduate theses finished (Ph.D) 3 Percentage of co-tutored theses with external 21% researchers Percentage of co-tutored theses with researchers of the 21% Project N° of national collaboration projects 2 N° of international collaboration projects 4 Number of stays/visits to other institutions by students 8 or researchers of the project National and Number of stays/visits in the project from students or International 24 collaboration researchers of other centers or projects N° of public or private(not enterprises) involved in the 24 project Percentage of publications Co-authored with external 80% researchers Nº of dissemination/extramural events 28 Nº of times the project appears in mass media 10 Total Nº of attendants to dissemination events 1500 Dissemination and extramural Nº of national academic attendants 300 activities Nº of international academic attendants 100 Nº of attendants from non-academic sectors 1100 N° of documents, reports, proceedings resulting from 6 dissemination/extramural events or activities