Computational Sciences Year 2016 Activity Report

Report (2016)

Born from a bottom-up initiative of Mathematics, Computer Science, Physics and Computational Engineering, Computational Sciences (CoSc) have contributed to create at UL a positive and symbiotic research ... [more ▼]

Born from a bottom-up initiative of Mathematics, Computer Science, Physics and Computational Engineering, Computational Sciences (CoSc) have contributed to create at UL a positive and symbiotic research environment relying on a strong fundamental scientific research core. CoSc will continue to rationalize research efforts across a range of strategic innovation domains by centralizing research and development tools and building upon the existing strengths of the Luxembourgish research and socio-economic landscape. [less ▲]

miRNAs in ancient tissue specimens of the Tyrolean Iceman

in Molecular Biology and Evolution (2016), 34(4), 793-801

The analysis of nucleic acids in ancient samples is largely limited to DNA. Small noncoding RNAs (microRNAs) are known to be evolutionary conserved and stable. To gain knowledge on miRNAs measured from ... [more ▼]

The analysis of nucleic acids in ancient samples is largely limited to DNA. Small noncoding RNAs (microRNAs) are known to be evolutionary conserved and stable. To gain knowledge on miRNAs measured from ancient samples, we profiled microRNAs in cryoconserved mummies. First, we established the approach on a World War One warrior, the “Kaiserj€ager”, which has been preserved for almost one century. Then, we profiled seven ancient tissue specimens including skeletal muscle, stomach mucosa, stomach content and two corpus organ tissues of the 5,300-year-old copper age mummy Iceman and compared these profiles to the presence of organ-specific miRNAs in modern tissues. Our analyses suggest the presence of specific miRNAs in the different Iceman’s tissues. Of 1,066 analyzed human miRNAs, 31 were discovered across all biopsies and 87 miRNAs were detected only in a single sample. To check for potential microbiological contaminations, all miRNAs detected in Iceman samples and not present in ancient samples were mapped to 14,582 bacterial and viral genomes. We detected few hits (3.9% of miRNAs compared with 3.6% of miRNAs). Interestingly, the miRNAs with higher abundance across all ancient tissues were significantly enriched for Guanine (P value of 10–13) and Cytosine (P value of 10–7). The same pattern was observed for modern tissues. Comparing miRNAs measured from ancient organs to modern tissue patterns highlighted significant similarities, e.g., formiRNAs present in themuscle. Our first comprehensive analysis of microRNAs in ancient human tissues indicates that these stable molecules can be detected in tissue specimens after 5,300 years. [less ▲]

Klaslokalen Binnenstebuiten: Leerkrachten over de veranderende onderwijsleeromgeving doorheen hun carrière (1960-2015)

Article for general public (2016)

Welke scholen hebben we nodig voor de 21ste eeuw? Hoe moeten die toekomstige schoolgebouwen eruitzien? Misschien wel als één grote open werkruimte – met zithoeken, labo’s, vergaderlokalen voor groepswerk ... [more ▼]

Welke scholen hebben we nodig voor de 21ste eeuw? Hoe moeten die toekomstige schoolgebouwen eruitzien? Misschien wel als één grote open werkruimte – met zithoeken, labo’s, vergaderlokalen voor groepswerk, een immer toegankelijke media- en bibliotheek, enzovoort – waarin leerkrachten en leerlingen vrij kunnen bewegen naar gelang de activiteiten en noden. Zullen de ‘traditionele’ klaslokalen hun bestaansredenen verliezen in deze nieuwe onderwijsleeromgevingen? Het vraagstuk naar innovatieve scholenbouw is verre van nieuw. Inderdaad, eb en vloed kenmerken onze onderwijsgeschiedenis.klaslokalen hun bestaansredenen verliezen in deze nieuwe onderwijsleeromgevingen? Het vraagstuk naar innovatieve scholenbouw is verre van nieuw. Inderdaad, eb en vloed kenmerken onze onderwijsgeschiedenis. [less ▲]

Nonequilibrium Thermodynamics of Chemical Reaction Networks: Wisdom from Stochastic Thermodynamics

in Physical Review X (2016), 6(4), 041064

We build a rigorous nonequilibrium thermodynamic description for open chemical reaction networks of <br /><br />elementary reactions. Their dynamics is described by deterministic rate equations with mass ... [more ▼]

We build a rigorous nonequilibrium thermodynamic description for open chemical reaction networks of <br /><br />elementary reactions. Their dynamics is described by deterministic rate equations with mass action <br /><br />kinetics. Our most general framework considers open networks driven by time-dependent chemostats. <br /><br />The energy and entropy balances are established and a nonequilibrium Gibbs free energy is introduced. <br /><br />The difference between this latter and its equilibrium form represents the minimal work done by the <br /><br />chemostats to bring the network to its nonequilibrium state. It is minimized in nondriven detailed-balanced <br /><br />networks (i.e., networks that relax to equilibrium states) and has an interesting information-theoretic <br /><br />interpretation. We further show that the entropy production of complex-balanced networks (i.e., networks <br /><br />that relax to special kinds of nonequilibrium steady states) splits into two non-negative contributions: one <br /><br />characterizing the dissipation of the nonequilibrium steady state and the other the transients due to <br /><br />relaxation and driving. Our theory lays the path to study time-dependent energy and information <br /><br />transduction in biochemical networks. [less ▲]

First-principles modeling of molecular crystals: structures and stabilities, temperature and pressure

in Wiley Interdisciplinary Reviews: Computational Molecular Science (2016)

The understanding of the structure, stability, and response properties of molecular crystals at finite temperature and pressure is crucial for the field of crystal engineering and their application. For a ... [more ▼]

The understanding of the structure, stability, and response properties of molecular crystals at finite temperature and pressure is crucial for the field of crystal engineering and their application. For a long time, the field of crystal-structure prediction and modeling of molecular crystals has been dominated by classical mechanistic force-field methods. However, due to increasing computational power and the development of more sophisticated quantum-mechanical approximations, first-principles approaches based on density functional theory can now be applied to practically relevant molecular crystals. The broad transferability of first-principles methods is especially imperative for polymorphic molecular crystals. This review highlights the current status of modeling molecular crystals from first principles. We give an overview of current state-of-the-art approaches and discuss in detail the main challenges and necessary approximations. So far, the main focus in this field has been on calculating stabilities and structures without considering thermal contributions. We discuss techniques that allow one to include thermal effects at a first-principles level in the harmonic or quasi-harmonic approximation, and that are already applicable to realistic systems, or will be in the near future. Furthermore, this review also discusses how to calculate vibrational and elastic properties. Finally, we present a perspective on future uses of first-principles calculations for modeling molecular crystals and summarize the many remaining challenges in this field. [less ▲]

Sproochepolitik: Et gëtt keng einfach Léisungen

Speeches/Talks (2016)

Household Nonemployment, Social Risks and Inequality in Europe

Doctoral thesis (2016)

The dissertation explores interactions between households, states and markets and their relation to socio-economic inequalities among working-age households. The focus lies on three aspects: the ... [more ▼]

The dissertation explores interactions between households, states and markets and their relation to socio-economic inequalities among working-age households. The focus lies on three aspects: the importance of the welfare state, economic risks and opportunities within households, and the link between these two aspects and broader patterns of inequality at the societal level. These are analysed in three empirical studies, using a range of statistical methods (multilevel analysis, event history models and counterfactual analyses of income distributions). In addition, an extensive framework paper provides a background to the analyses, clarifies their relation in theoretical terms, and discusses the results. The first empirical study explores the relation between the regulation of social benefits, social risks, and household nonemployment in 20 European countries using internationally comparative institutional and survey data. The study reveals that eligibility conditions and activation policy vary systematically with the effect of social risks on the probability of household nonemployment. The strength and direction of influence depends on the specific policy area and risk factor. The second study analyses the duration of household nonemployment for British and German couples from the early 1990s to the mid-2000s. Dual joblessness has become longer over time, which is related to changes in the household composition of nonemployed couples. The third analysis evaluates the consequences of welfare shifts between households on changing patterns of inequality between 2005 and 2010. Changes in the distribution of household employment, benefit transfers, and family types in Germany, the United Kingdom, Poland, and Spain are analysed in terms of their contribution to developments in income inequality between households. The analysis of income distributions suggests that changes in socio-demographic and economic household characteristics in a population can have a substantial impact on different income groups. The overarching conclusion of the dissertation is that certain aspects of household composition enhance the risk of lower economic activity and welfare but that the impact of these factors varies strongly according to the broader context the households are situated in. Social policies that have the potential to reduce inequalities between households need to consider possible adverse effects on economic risk structures and spill-over effects to other areas of social protection. Future research should continue studying the household’s role in relation to the market, the state, and individual needs and resources; incorporate additional economic and welfare regime aspects into the analyses; and explore further statistical tools to do so. [less ▲]

On horizontal and vertical categorifications of Leibniz algebras

Presentation (2016, December 16)

Systems Biology through the Concept of Emergence

in Green, Sarah (Ed.) Philosophy of Systems Biology: Perspectives from Scientists and Philosophers (History, Philosophy and Theory of the Life Sciences) (2016)

Diagnostic Competencies of Teachers: Accuracy of Judgement, Sources of Biases, and Consequences of (Mis-) Judgement

Doctoral thesis (2016)

Educational assessment tends to rely on more or less standardized tests, teacher judgments, and observations. Although teachers spend approximately half of their professional conduct in assessment-related ... [more ▼]

Educational assessment tends to rely on more or less standardized tests, teacher judgments, and observations. Although teachers spend approximately half of their professional conduct in assessment-related activities, most of them enter their professional life unprepared, as classroom assessment is often not part of their educational training. Since teacher judgments matter for the educational development of students, the judgments should be up to a high standard. The present dissertation comprises three studies focusing on accuracy of teacher judgments (Study 1), consequences of (mis-)judgment regarding teacher nomination for gifted programming (Study 2) and teacher recommendations for secondary school tracks (Study 3), and individual student characteristics that impact and potentially bias teacher judgment (Studies 1 through 3). All studies were designed to contribute to a further understanding of classroom assessment skills of teachers. Overall, the results implied that, teacher judgment of cognitive ability was an important constant for teacher nominations and recommendations but lacked accuracy. Furthermore, teacher judgments of various traits and school achievement were substantially related to social background variables, especially the parents’ educational background. However, multivariate analysis showed social background variables to impact nomination and recommendation only marginally if at all. All results indicated differentiated but potentially biased teacher judgments to impact their far-reaching referral decisions directly, while the influence of social background on the referral decisions itself seems mediated. Implications regarding further research practices and educational assessment strategies are discussed. The implications on the needs of teachers to be educated on judgment and educational assessment are of particular interest and importance. [less ▲]