Efficient Forward Simulation of Fisher-Wright Populations with Stochastic Population Size and Neutral Single Step Mutations in Haplotypes

In both population genetics and forensic genetics it is important to know how haplotypes are distributed in a population. Simulation of population dynamics helps facilitating research on the distribution of haplotypes. In forensic genetics, the haplotypes can for example consist of lineage markers such as short tandem repeat loci on the Y chromosome (Y-STR). A dominating model for describing population dynamics is the simple, yet powerful, Fisher-Wright model. We describe an efficient algorithm for exact forward simulation of exact Fisher-Wright populations (and not approximative such as the coalescent model). The efficiency comes from convenient data structures by changing the traditional view from individuals to haplotypes. The algorithm is implemented in the open-source R package 'fwsim' and is able to simulate very large populations. We focus on a haploid model and assume stochastic population size with flexible growth specification, no selection, a neutral single step mutation process, and self-reproducing individuals. These assumptions make the algorithm ideal for studying lineage markers such as Y-STR.Comment: 17 pages, 6 figure

Lattice Interferometer for Ultra-Cold Atoms

We demonstrate an atomic interferometer based on ultra-cold atoms released from an optical lattice. This technique yields a large improvement in signal to noise over a related interferometer previously demonstrated. The interferometer involves diffraction of the atoms using a pulsed optical lattice. For short pulses a simple analytical theory predicts the expected signal. We investigate the interferometer for both short pulses and longer pulses where the analytical theory break down. Longer pulses can improve the precision and signal size. For specific pulse lengths we observe a coherent signal at times that differs greatly from what is expected from the short pulse model. The interferometric signal also reveals information about the dynamics of the atoms in the lattice. We investigate the application of the interferometer for a measurement of $h/m_A$ that together with other well known constants constitutes a measurement of the fine structure constant

Referencehåndtering med Mendeley:mellem organisering, skrivning og samarbejde

DK AbstractReferencehåndteringsværktøjer har eksisteret længe, men har med web 2.0-bølgen fået fornyet aktualitet. Fra at være digitale redskaber der automatiserer det møjsomme arbejde med at citere kilder, er de i dag avancerede applikationer med både læse, produktions- og delingsfunktioner. Til trods for, at der findes et omfangsrigt materiale, der introducerer og sammenligner på teknisk niveau, er der et opsigtsvækkende fravær af undersøgelser, der interesserer sig for læringsaspekterne. I denne artikel diskuteres det, med udgangspunkt i programmet Mendeley, hvordan man kan benytte referencehåndteringsværktøjer som lærings- og forskningsredskab og ikke udelukkende til effektivisering af arbejdsprocesser. Det diskuteres hvordan Mendeley kan bidrage til: 1. organisering og reartikulering af forskningsspørgsmål; 2. hvordan samskabelse faciliteres gennem fælles kildesamlinger; samt 3. hvorledes det tekstnære tænkearbejde kan styrkes ved, at afstanden mellem egen og andres tekster mindskes. Det konkluderes at Mendeley har anvendelsespotentiale til at understøtte almene videnskabelige aktiviteter som videnkonstruktion, videnproduktion og videndeling med kildemateriale som omdrejningspunkt. EN AbstractReference management software have existed for some time, but have regained relevance in the wake for web 2.0. From being digital tools for automating the tiresome work of citing sources, they are today multifaceted applications with reading, production and sharing functionalities. In spite a vast amount of material introducing and comparing reference management software on a technical basis, there is a surprising lack of studies interested in learning aspects. With the software Mendeley as case, this article discuss’ how reference management software can be applied as learning and research tools, not solely to increase workflows efficiency. It’s debated Mendeley can support; 1. Organizing and rearticulating of research questions and frameworks; 2. How co-creation is facilitated via joint collections; and 3. How thinking about textual relations can be strengthened by diminishing the distance between own and others’ texts. It is concluded that Mendeley has potential to support regular scientific activities such as knowledge construction, production and sharing, with literature as its fulcrum