Kinetics of target site localization of a protein on DNA: a stochastic approach

It is widely recognized that the cleaving rate of a restriction enzyme on target DNA sequences is several orders of magnitude faster than the maximal one calculated from the diffusion--limited theory. It was therefore commonly assumed that the target site interaction of a restriction enzyme with DNA has to occur via two steps: one--dimensional diffusion along a DNA segment, and long--range jumps coming from association/dissociation events. We propose here a stochastic model for this reaction which comprises a series of 1D diffusions of a restriction enzyme on non-specific DNA sequences interrupted by 3D excursions in the solution until the target sequence is reached. This model provides an optimal finding strategy which explains the fast association rate. Modeling the excursions by uncorrelated random jumps, we recover the expression of the mean time required for target site association to occur given by Berg & al. \cite{berg81}, and we explicitly give several physical quantities describing the stochastic pathway of the enzyme. For competitive target sites we calculate two quantities: processivity and preference. By comparing these theoretical expressions to recent experimental data obtained for \textit{Eco}RV--DNA interaction, we quantify: i) the mean residence time per binding event of \textit{Eco}RV on DNA for a representative 1D diffusion coefficient, ii) the average lengths of DNA scanned during the 1D diffusion (during one binding event and during the overall process), iii) the mean time and the mean number of visits needed to go from one target site to the other. Further, we evaluate the dynamics of DNA cleavage with regard to the probability for the restriction enzyme to perform another 1D diffusion on the same DNA substrate following a 3D excursion.Comment: 10 pages, 8 figure

Economic solutions are crucial to help solve Somalia’s political woes

Maximilien von Berg argues that a formalised and inclusive financial sector is necessary for Somalia’s political and economic prospects to improve.

Cultivating the civic identities and agency of undergraduates at a university in the UK

In recent years, many universities in the UK have claimed that citizenship is a benefit of attending their institution. This is at odds with the changed landscape of higher education which incentivises students in a competitive pursuit of valued grades and experiences for CVs to attain well paid employment. This study aims to discover what form of citizenship education can help nurture civic identities and agency of students at university. There is a lack of research on how citizenship education can achieve this in the marketised environment of UK universities and as part of a teacher’s professional practice at university. This study used an action research approach and an interpretive framework of analysis that drew on Friere’s ideas of authentic reflection, Mezirow’s theory of transformational learning and Boal’s forms of Forum and Image Theatre. This involved a series of activities combining discussion of personal beliefs, norms and values, critical incidents with marginalised groups in society, and, experimentation with issues from the students own lives in Forum Theatre. The findings show the development of an inexclusive sense of community premised on solidarity. This arose from reversing processes of othering and reduced senses of loneliness at university, which created potential for collective agency. The crucial medium was experiences of empathy and compassion followed up by critical and authentic reflection in liminal spaces. This process is termed ‘felt and attentive practice’, a rethinking of how civic identity entwines with civic agency that produces powerful examples of deep learning of civic identity. A liminal space away from the pressures of study facilitated felt and attentive practice even though some students attended to improve their CVs. The approach trialled here offers potential for a new form of professional practice that stimulates self and social awareness, expands collective agency and aids transition to university for students

Signatures of topological Josephson junctions

Quasiparticle poisoning and diabatic transitions may significantly narrow the window for the experimental observation of the $4\pi$-periodic $dc$ Josephson effect predicted for topological Josephson junctions. Here, we show that switching current measurements provide accessible and robust signatures for topological superconductivity which persist in the presence of quasiparticle poisoning processes. Such measurements provide access to the phase-dependent subgap spectrum and Josephson currents of the topological junction when incorporating it into an asymmetric SQUID together with a conventional Josephson junction with large critical current. We also argue that pump-probe experiments with multiple current pulses can be used to measure the quasiparticle poisoning rates of the topological junction. The proposed signatures are particularly robust, even in the presence of Zeeman fields and spin-orbit coupling, when focusing on short Josephson junctions. Finally, we also consider microwave excitations of short topological Josephson junctions which may complement switching current measurements.Comment: 25 pages, 13 figures. Accepted by Phys. Rev.

Does corruption matter?

Globalization and more open economies has over the last two decades led to an increase of FDI which has been argued to lead to economic growth. So far economists are not unanimous on to what extent or fully agreed upon if certain other conditions have to be fulfilled for this to be true. In newer research on economic development scientists emphasize the importance of institutions for economic growth. The interaction between institutions and other variables affecting economic growth has become more important to understand, especially in developing countries. This thesis is examining if FDI affect economic growth in developing countries and if there is an interaction between FDI and corruption affecting economic growth. Knowing how institutions affect development will make it easier to know which measures that needs to be taken to achieve better conditions for economic growth. The focus and research questions are following: • Does FDI affect economic growth in developing countries? • Is there an interaction effect between FDI and informal institutions affecting economic growth? One key finding is that FDI have a positive effect on economic growth. Additionally, when a possible interaction effect between FDI inflow and corruption is taken into consideration, no significant results are found. As this thesis however only covers developing countries a higher significance level can be argued to be tolerated, and two trends have been found: higher levels of corruption make FDI have a less positive effect on economic growth, and the more FDI a country receive, the worse corruption is for economic growth. The area can and should be explored further and more research is needed before any stronger conclusions can be made

Higher Education and Female Labour Market Participation

While female labour market participation is increasing worldwide, the development in Chile is slow and concentrated to the capital city of Santiago de Chile. Education has been found to increase female labour market participation in several studies, where my thesis contributes to the research with more careful analysis of the effects of higher education. Rather than analysing the joint effect of higher education, I disentangle the effects of different types of institutions of higher education, which allows me to analyse each corresponding effect on female labour market participation. By using data from the national census, and comparing results from the probit model and the linear probability model, I show that university education has the highest effect on female labour market participation, that education at technical centres has a slightly smaller effect, and that education at professional institutes has the smallest effect. Furthermore, by complimenting the thesis with my minor field study (MFS) about women’s policy preferences, I am able to discuss policy implementation with better foundation and support than studies that only rely on economic theory. My results suggest that policies that aim to simplify a combination of family life and career may be an efficient way to increase female labour market participation among women with higher education, where the MFS emphasise work concerning the quality of day care centres. Lastly, the highest valued policy in the MFS is work aiming to reduce the gender wage gap, which when implemented may decrease the impact of cultural values on labour market decisions, and thus further increase labour market participation among women with higher education. Key words: Higher education, female labour market participation, policy preferences, probit model, linear probability model

Marketable Wealth in a Poor African Country

The study uses an asset index of consumer durables to track changes in household wealth in Ghana during the recent period of strong growth. Using the Ghana Living Standards Survey of 1998 that contains both wealth data and consumer durable data, the authors demonstrate that the asset index approximate marketable wealth adequately. Although asset index estimates of wealth cannot match the precision of wealth surveys,this approach can provide useful information on marketable wealth in countries where more appropriate sources are not available. The asset index analysis with the three demographic and health surveys for 1993, 1998 and 2003 suggests that the solid economic growth seen over this period has been accompanied by a strong rise in the average asset index scores.wealth, Ghana, asset index

Marketable Wealth in a Poor African Country: Using an index of consumer durables to investigate wealth accumulation by households in Ghana

wealth, Ghana, asset index

Comparative Study of Multicanonical and Simulated Annealing Algorithms in the Protein Folding Problem

We compare a few variants of the recently proposed multicanonical method with the well known simulated annealing for the effectiveness in search of the energy global minimum of a biomolecular system. For this we study in detail Met-enkephalin, one of the simplest peptides. We show that the new method not only outperforms simulated annealing in the search of the energy groundstate but also provides more statistical-mechanical information about the system.Comment: to be published in Physica A, LATEX 32 pages, figures available on reques

Multi-Overlap Simulations for Transitions between Reference Configurations

We introduce a new procedure to construct weight factors, which flatten the probability density of the overlap with respect to some pre-defined reference configuration. This allows one to overcome free energy barriers in the overlap variable. Subsequently, we generalize the approach to deal with the overlaps with respect to two reference configurations so that transitions between them are induced. We illustrate our approach by simulations of the brainpeptide Met-enkephalin with the ECEPP/2 energy function using the global-energy-minimum and the second lowest-energy states as reference configurations. The free energy is obtained as functions of the dihedral and the root-mean-square distances from these two configurations. The latter allows one to identify the transition state and to estimate its associated free energy barrier.Comment: 12 pages, (RevTeX), 14 figures, Phys. Rev. E, submitte