Exploring unfrequent events with accelerated molecular dynamics simulations: from photochemistry to drug design

La meva incorporació al grup de recerca del Prof. McCammon (University of California San Diego) en qualitat d’investigador post doctoral amb una beca Beatriu de Pinós, va tenir lloc el passat 1 de desembre de 2010; on vaig dur a terme les meves tasques de recerca fins al darrer 1 d’abril de 2012. El Prof. McCammon és un referent mundial en l’aplicació de simulacions de dinàmica molecular (MD) en sistemes biològics d’interès humà. La contribució més important del Prof. McCammon en la simulació de sistemes biològics és el desenvolupament del mètode de dinàmiques moleculars accelerades (AMD). Les simulacions MD convencionals, les quals estan limitades a l’escala de temps del nanosegon (~10-9s), no son adients per l’estudi de sistemes biològics rellevants a escales de temps mes llargues (μs, ms...). AMD permet explorar fenòmens moleculars poc freqüents però que son clau per l’enteniment de molts sistemes biològics; fenòmens que no podrien ser observats d’un altre manera. Durant la meva estada a la “University of California San Diego”, vaig treballar en diferent aplicacions de les simulacions AMD, incloent fotoquímica i disseny de fàrmacs per ordinador. Concretament, primer vaig desenvolupar amb èxit una combinació dels mètodes AMD i simulacions Car-Parrinello per millorar l’exploració de camins de desactivació (interseccions còniques) en reaccions químiques fotoactivades. En segon lloc, vaig aplicar tècniques estadístiques (Replica Exchange) amb AMD en la descripció d’interaccions proteïna-lligand. Finalment, vaig dur a terme un estudi de disseny de fàrmacs per ordinador en la proteïna-G Rho (involucrada en el desenvolupament de càncer humà) combinant anàlisis estructurals i simulacions AMD. Els projectes en els quals he participat han estat publicats (o estan encara en procés de revisió) en diferents revistes científiques, i han estat presentats en diferents congressos internacionals. La memòria inclosa a continuació conté més detalls de cada projecte esmentat.

Characterization and evolution of the novel gene family FAM90A in primates originated by multiple duplication and rearrangement events

Genomic plasticity of human chromosome 8p23.1 region is highly influenced by two groups of complex segmental duplications (SDs), termed REPD and REPP, that mediate different kinds of rearrangements. Part of the difficulty to explain the wide range of phenotypes associated with 8p23.1 rearrangements is that REPP and REPD are not yet well characterized, probably due to their polymorphic status. Here, we describe a novel primate-specific gene family, named FAM90A (family with sequence similarity 90), found within these SDs. According to the current human reference sequence assembly, the FAM90A family includes 24 members along 8p23.1 region plus a single member on chromosome 12p13.31, showing copy number variation (CNV) between individuals. These genes can be classified into subfamilies I and II, which differ in their upstream and 5′-untranslated region sequences, but both share the same open reading frame and are ubiquitously expressed. Sequence analysis and comparative fluorescence in situ hybridization studies showed that FAM90A subfamily II suffered a big expansion in the hominoid lineage, whereas subfamily I members were likely generated sometime around the divergence of orangutan and African great apes by a fusion process. In addition, the analysis of the Ka/Ks ratios provides evidence of functional constraint of some FAM90A genes in all species. The characterization of the FAM90A gene family contributes to a better understanding of the structural polymorphism of the human 8p23.1 region and constitutes a good example of how SDs, CNVs and rearrangements within themselves can promote the formation of new gene sequences with potential functional consequences.

External sources of innovation and industry-university interaction:evidence from Spanish firms

This paper is about the firm innovation process and the cooperation of the innovative firms with other firms and public institutions. A special attention is paid to the cooperation with universities. We use the Technological Innovation Survey (TIS) from the Instituto Nacional de Estadística (Spain) in order to obtain data for 4,159 innovative firms. Our results show that firm's cooperation activities are closely linked to the characteristics of the industry and the firm as well as to the origin of public funds for R&D activities. Key words: Innovation, universities, Spanish economy. JEL code: O31, I20, L60

Sabbatical stay at CREVER, University Rovira i Virgili

A three-year research proposal of international impact and quality was developed between the author and CREVER researchers, taking into account the infrastructure and research lines already being carried out at CREVER. The project is related to the study of new mixtures in thermal activated systems, by the addition of a third component to help the heat transfer processes. The project proposes the use of water and lithium nitrate as absorbents in ternary ammonia mixtures, varying the concentration with the objective of optimising the mixture for solar air conditioning purposes. Also, the research proposal will promote an intensive collaboration in the following years between CREVER and The Centro de Investigación en Energía-UNAM, Mexico.

Not all university degrees yield the same return: private and social returns to higher education for males in Spain

In this paper we use micro data from the Spanish Family Expenditure Survey for 1990 to estimate, for the first time, the private and social rates of return of different university degrees in Spain. We compute internal rates of return and include investment on higher education financed by the public purse to estimate social rates of return. Our main finding is that, as presumed, there is large heterogeneity in rates of return amongst different university

Memòria: estada a London South Bank University (Regne Unit)

Investigación producida a partir de una estancia en la London South Bank University, Reino Unido, entre los meses de setiembre y diciembre del 2005. Se estudia el trabajo sexual en el Reino Unido desde tres perspectivas diferentes. Por una parte, se trata la historia del feminismo anglosajón respecto a sus visiones sobre la prostitución, desde una aproximación a las fuentes. Por otra parte, se plantea la situación jurídico-política. Finalmente, se presenta brevemente a las principales entidades que dan apoyo al colectivo de trabajadoras del sexo en la ciudad de Londres.

Technological trampolines for new venture creation in Catalonia: the case of the University of Girona

Recent trends in technology transfer show an intensification of spin-off creation as a modality of university research commercialisation, complementary to the conventional ones, contract research and licensing. In this paper we analyse the evolution, objectives, resources and activities of a specialised unit –Technological Trampoline (TT) - in charge of new venture creation at the University of Girona (Catalonia-Spain). Based on two theoretical frameworks, Resource-based-view and Institutional Theory, we adopt a multi-dimensional approach to study the strategy of spinning-off new ventures at the University of Girona in terms of resources and activities, how this process is organised and if the outputs fit with this UdG’s objectives and the local environment. Our main contribution is an in-depth analysis of the spin-off creation unit with special emphasis on its variety of resources and activities. The results have a series of implications and recommendations at both university and TT level.

Tot repensant els serveis bibliogràfics a la University of California

Informe d'un Grup de Treball sobre Serveis Bibliogràfics de la University of California que presenta un seguit de recomanacions sobre els canvis que aquests serveis haurien d'implementar per millorar les seves prestacions. Els autors posen de manifest el desfasament que pateixen bona part dels serveis bibliotecaris actuals davant les prestacions que ofereixen portals com Amazon o Google. Les recomanacions s'estructuren en quatre apartats: millorar la cerca i la recuperació, redissenyar l'OPAC, adoptar noves pràctiques catalogràfiques i donar suport a la millora continua. L'informe finalitza amb l'enumeració d'una seixantena de possibles actuacions addicionals que també es van considerar i les raons per les quals finalment es van descartar.

Memòria justificativa del treball realitzat durant l'estada a la University of California at Los Angeles (UCLA)

Projecte de recerca elaborat a partir d’una estada a la Graduate School of Education and Information Studies (GSEIS) de la University of California at Los Angeles (UCLA), Estats Units, entre gener i juny del 2007. En el context d’elaboració d’una futura tesi doctoral sobre la metodologia comunicativa crítica i la interacció persona-ordinador, la intenció ha estat aprofundir des d'una perspectiva internacional. La GSEIS i la UCLA en general conta amb innumerables recursos bibliogràfics així com amb professorat de reconegut prestigi internacional en la recerca vinculada a la barreja de temes com l'educació, la inclusió i la transformació social, la Comunicació, les TIC i el disseny de la Interacció Persona Ordinador; integració de disciplines en la que es mou la meva tesi doctoral. La possibilitat d'accedir a la Young Research Library, així com l'assistència a diverses conferències relacionades amb el meu àmbit d'estudi, la celebració de diverses tutories amb professorat de la GSEIS i d'altres departaments de la UCLA, i la invitació a participar del seminari de doctorat del professor Douglas Kellner, han contribuït de forma remarcable al meu projecte amb: aportacions de la literatura internacional i nombrosos exemples de bones pràctiques de projectes vinculats al Participatory Design com a metodologia en si mateixa desvinculada del Disseny Centrat en l'Usuari, un dels aspectes centrals de la meva tesi. Amb tot això vaig poder reforçar i desenvolupar quatre dels capítols de la meva dissertació, concretament els relacionats amb el context social i metodològic, i els que presenten el disseny de la Interacció Persona ordinador des d'un enfocament general així com el que es centra en el Disseny participatiu i les seves vinculacions amb la metodologia comunicativa crítica.

Incentives in university technology transfers

There are two main ways in which the knowledge created in universities has been transferred to firms: licensing agreements and the creation of spin-offs. In this paper, we describe the main steps in the transfer of university innovations, the main incentive issues that appear in this process, and the contractual solutions proposed to address them.

The determinants of university patenting: Do incentives matter?

In recent years various studies have examined the factors that may explain academic patents. Existing analyses have also underlined the substantial differences to be found in European countries in the institutional framework that defines property rights for academic patents. The objective of this study is to contribute to the empirical literature on the factors explaining academic patents and to determine whether the incentives that universities offer researchers contribute towards explaining the differences in academic patenting activity. The results of the econometric analysis for the Spanish universities point towards the conclusion that the principal factor determining the patents is funding of R&D while royalty incentives to researchers do not appear to be significant.

Which firms want PhDs? The effect of the university-industry relationship on the PhD labour market

PhD graduates hold the highest education degree, are trained to conduct research and can be considered a key element in the creation, commercialization and diffusion of innovations. The impact of PhDs on innovation and economic development takes place through several channels such as the accumulation of scientific capital stock, the enhancement of technology transfers and the promotion of cooperation relationships in innovation processes. Although the placement of PhDs in industry provides a very important mechanism for transmitting knowledge from universities to firms, information about the characteristics of the firms that employ PhDs is very scarce. The goal of this paper is to improve understanding of the determinants of the demand for PhDs in the private sector. Three main potential determinants of the demand for PhDs are considered: cooperation between firms and universities, R&D activities of firms and several characteristics of firms, size, sector, productivity and age. The results from the econometric analysis show that cooperation between firms and universities encourages firms to recruit PhDs and point to the existence of accumulative effects in the hiring of PhD graduates.

Recerca versus docència en una experiència d'internalització dels estudis de Geografia a la Universitat de Girona: The faces of landscape, Catalonia and North Karelia = Research versus teaching in one experience of internationalization of the Geography degree studies in the University of Girona: The faces of landscape, Catalonia and North Karelia

Un dels reptes cabdals de la Universitat és enllaçar l’experiència de recerca amb la docència, així com promoure la internacionalització dels estudis, especialment a escala europea, tenint present que ambdues poden actuar com a catalitzadores de la millora de la qualitat docent. Una de les fórmules d’internacionalització és la realització d’assignatures compartides entre universitats de diferents països, fet que suposa l’oportunitat d’implementar noves metodologies docents. En aquesta comunicació es presenta una experiència en aquesta línia desenvolupada entre la Universitat de Girona i la Universitat de Joensuu (Finlàndia) en el marc dels estudis de Geografia amb la realització de l’assignatura 'The faces of landscape: Catalonia and North Karelia'. Aquesta es desenvolupa al llarg de dues setmanes intensives, una en cadascuna de les Universitats. L’objectiu és presentar i analitzar diferents significats del concepte paisatge aportant també metodologies d’estudi tant dels aspectes físics i ecològics com culturals que s’hi poden vincular i que són les que empren els grups de recerca dels professors responsables de l’assignatura. Aquesta part teòrica es completa amb una presentació de les característiques i dinàmiques pròpies dels paisatges finlandesos i catalans i una sortida de camp. Per a la part pràctica es constitueixen grups d’estudi multinacionals que treballen a escala local algun dels aspectes en els dos països, es comparen i es realitza una presentació i defensa davant del conjunt d’estudiants i professorat. La llengua vehicular de l’assignatura és l’anglès.

Power laws and scaling of rain events and dry spells in the Catalonia region

We analyze the statistics of rain-event sizes, rain-event durations, and dry-spell durations in a network of 20 rain gauges scattered in an area situated close to the NW Mediterranean coast. Power-law distributions emerge clearly for the dryspell durations, with an exponent around 1.50 ± 0.05, although for event sizes and durations the power-law ranges are rather limited, in some cases. Deviations from power-law behavior are attributed to finite-size effects. A scaling analysis helps to elucidate the situation, providing support for the existence of scale invariance in these distributions. It is remarkable that rain data of not very high resolution yield findings in agreement with self-organized critical phenomena.

Higher education as formation of the self and citizenship: an ethnography of the University Students from Amman, Jordan

My interest in higher education and citizenship in the Middle East at large and in Jordan in particular is fostered by some of the reflections Eickelman proposed (1992). Being a quite recent phenomenon, intimately linked with the more general topic of state formation it seemed to me more suitable to study it in a little country with a recent history (a field study left almost unexplored until now as far as Jordan is concerned, to the best of my knowledge, since Antoun 1994 focuses on the migration as a quest for higher education). The process of state formation in Jordan is quite studied. I thus intended to study the higher education policies as an attempt both to create a national citizenry and more recently as a way of controlling the more problematic part of the population (youth, which constitutes more than the double of the population. See UNDP and Ministry of Planning 2000). How do the young students enter the university system, and in which way does this system work? How is this system designed, in order to retain social control of the students (since they are usually perceived to be a factor of social and political instability, as in Iran or in Egypt)? Is there any significant difference between different faculties? And if so, why? My conclusions at this stage are that the university system is an integral part of the survival of the regime. The system works quite well, and Jordan has one of the best educational position in the region. Yet there are important distinctions to be made: the access to the better faculties is socially selective while the less valued faculties are left to the poorer and less wealthy youth. This results in a different treatment of the students and of the courses that I analysed. In the better faculties the teaching standards are quite high, and the relationship between professors and students is almost on a same-level base, while in the less privileged faculties the opposite is true. Thus we can observe a concrete politics of divide et impera intended to split the youth in two. For the more privileged there are some freedoms, both within and outside classes, designed I guess at forging them as autonomous individuals. On the opposite the less privileged are kept under tight control, even if also these students are a privileged category among youth at large.