Hidden breakpoints in genome alignments

During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain and loss occurs in addition to other types of rearrangement, breakpoints of rearrangement can exist that are only detectable by comparison of three or more genomes. An arbitrarily large number of these "hidden" breakpoints can exist among genomes that exhibit no rearrangements in pairwise comparisons. We present an extension of the multichromosomal breakpoint median problem to genomes that have undergone gene gain and loss. We then demonstrate that the median distance among three genomes can be used to calculate a lower bound on the number of hidden breakpoints present. We provide an implementation of this calculation including the median distance, along with some practical improvements on the time complexity of the underlying algorithm. We apply our approach to measure the abundance of hidden breakpoints in simulated data sets under a wide range of evolutionary scenarios. We demonstrate that in simulations the hidden breakpoint counts depend strongly on relative rates of inversion and gene gain/loss. Finally we apply current multiple genome aligners to the simulated genomes, and show that all aligners introduce a high degree of error in hidden breakpoint counts, and that this error grows with evolutionary distance in the simulation. Our results suggest that hidden breakpoint error may be pervasive in genome alignments.Comment: 13 pages, 4 figure

High-dimensional quantum dynamics of adsorption and desorption of H2_2 at Cu(111)

We performed high-dimensional quantum dynamical calculations of the dissociative adsorption and associative desorption of hydrogen on Cu(111). The potential energy surface (PES) is obtained from density functional theory calculations. Two regimes of dynamics are found, at low energies sticking is determined by the minimum energy barrier, at high energies by the distribution of barrier heights. Experimental results are well-reproduced qualitatively, but some quantitative discrepancies are identified as well.Comment: 4 two column pages, revtex, 4 figures, to appear in Phys. Rev. Let

AI as a legal person

Abstract: The idea of the legal personhood of artificial intelligence (AI) — the idea that intelligent agents can have rights and incur obligations under the law— is controversial, and in fact is often dismissed out of hand: in this paper I will argue that, on the contrary, such legal personhood may be the next big challenge for our legal systems, and we need it to deal with the new kinds ofcomplexity introduced by AI. Furthermore, I argue that we already have experiences we can look: to this end we can draw on the reasoning applied to the legal personhood recognized for corporations and other nonhuman entities. In order to do this, I address some of the criticisms against ascribing legal personhood to AI. I also look at the Canadian and EU ethical guidelines so as to keep the development of AI within the framework of human values, and I show that an ascription of legal personhood to AI is consistent with them. I also address a few of the big issues involved in making the legal personhood of AI a reality.This paper is part of the project supported by the CONEX programme and has received funding from the Universidad Carlos III de Madrid, the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement N. 600371, el Ministerio de Economia, Industria y Competitividad (COFUND2014-51509), el Ministerio de Educacion, Cultura y Deporte (CEI-15-17) and Banco SantanderUniversidad Carlos III de Madrid (APC. Read & Publish Agreement CRUE-CSIC 2023

Rotation of hydrogen molecules during the dissociative adsorption on the Mg(0001) surface: A first-principles study

Using first-principles calculations, we systematically study the potential energy surfaces and dissociation processes of the hydrogen molecule on the Mg(0001) surface. It is found that during the dissociative adsorption process with the minimum energy barrier, the hydrogen molecule firstly orients perpendicular, and then rotates to be parallel to the surface. It is also found that the orientation of the hydrogen molecule at the transition state is neither perpendicular nor parallel to the surface. Most importantly, we find that the rotation causes a reduction of the calculated dissociation energy barrier for the hydrogen molecule. The underlying electronic reasons for the rotation of the hydrogen molecule is also discussed in our paper.Comment: 14 pages, 4 figure

Random division of an interval

The well-known relation between random division of an interval and the Poisson process is interpreted as a Laplace transformation. With the use of this interpretation a number of (in part known) results is derived very easily

Aharonov-Bohm-like effect for light propagating in nematics with disclinations

Using a geometric approach for the propagation of light in anisotropic media, we investigate what effect the director field of disclinations may have on the polarization state of light. Parallel transport around the defect, of the spinor describing the polarization, indicates the acquisition of a topological phase, in analogy with the Aharonov-Bohm effect.Comment: 6 pages, to appear in Europhysics Letter

Transforming teacher education, an activity theory analysis

This paper explores the work of teacher education in England and Scotland. It seeks to locate this work within conflicting socio-cultural views of professional practice and academic work. Drawing on an activity theory framework that integrates the analysis of these contradictory discourses with a study of teacher educators’ practical activities, including the material artefacts that mediate the work, the paper offers a critical perspective on the social organisation of university-based teacher education. Informed by Engeström’s activity theory concept of transformation, the paper extends the discussion of contradictions in teacher education to consider the wider socio-cultural relations of the work. The findings raise important questions about the way in which teacher education work within universities is organised and the division of labour between schools and universities