Variational ground states of 2D antiferromagnets in the valence bond basis

We study a variational wave function for the ground state of the two-dimensional S=1/2 Heisenberg antiferromagnet in the valence bond basis. The expansion coefficients are products of amplitudes h(x,y) for valence bonds connecting spins separated by (x,y) lattice spacings. In contrast to previous studies, in which a functional form for h(x,y) was assumed, we here optimize all the amplitudes for lattices with up to 32*32 spins. We use two different schemes for optimizing the amplitudes; a Newton/conjugate-gradient method and a stochastic method which requires only the signs of the first derivatives of the energy. The latter method performs significantly better. The energy for large systems deviates by only approx. 0.06% from its exact value (calculated using unbiased quantum Monte Carlo simulations). The spin correlations are also well reproduced, falling approx. 2% below the exact ones at long distances. The amplitudes h(r) for valence bonds of long length r decay as 1/r^3. We also discuss some results for small frustrated lattices.Comment: v2: 8 pages, 5 figures, significantly expanded, new optimization method, improved result

A simple interpretation of quantum mirages

In an interesting new experiment the electronic structure of a magnetic atom adsorbed on the surface of Cu(111), observed by STM, was projected into a remote location on the same surface. The purpose of the present paper is to interpret this experiment with a model Hamiltonian, using ellipses of the size of the experimental ones, containing about 2300 atoms. The charge distribution for the different wavefunctions is analyzed, in particular, for those with energy close to the Fermi energy of copper Ef. Some of them show two symmetric maxima located on the principal axis of the ellipse but not necessarily at the foci. If a Co atom is adsorbed at the site where the wavefunction with energy $E_F$ has a maximum and the interaction is small, the main effect of the adsorbed atom will be to split this particular wavefunction in two. The total charge density will remain the same but the local density of states will present a dip at Ef at any site where the charge density is large enough. We relate the presence of this dip to the observation of quantum mirages. Our interpretation suggests that other sites, apart from the foci of the ellipses, can be used for projecting atomic images and also indicates the conditions for other non magnetic adsorbates to produce mirages.Comment: 3 pages, 3 Fig

How Xenopus laevis embryos replicate reliably: investigating the random-completion problem

DNA synthesis in \textit{Xenopus} frog embryos initiates stochastically in time at many sites (origins) along the chromosome. Stochastic initiation implies fluctuations in the time to complete and may lead to cell death if replication takes longer than the cell cycle time ($\approx 25$ min). Surprisingly, although the typical replication time is about 20 min, \textit{in vivo} experiments show that replication fails to complete only about 1 in 300 times. How is replication timing accurately controlled despite the stochasticity? Biologists have proposed two solutions to this "random-completion problem." The first solution uses randomly located origins but increases their rate of initiation as S phase proceeds, while the second uses regularly spaced origins. In this paper, we investigate the random-completion problem using a type of model first developed to describe the kinetics of first-order phase transitions. Using methods from the field of extreme-value statistics, we derive the distribution of replication-completion times for a finite genome. We then argue that the biologists' first solution to the problem is not only consistent with experiment but also nearly optimizes the use of replicative proteins. We also show that spatial regularity in origin placement does not alter significantly the distribution of replication times and, thus, is not needed for the control of replication timing.Comment: 16 pages, 9 figures, submitted to Physical Review

Mediation in the Law Curriculum

Cited by Lord Neuberger in ‘Educating Future Mediators’ at the 4th Civil Mediation Council National Conference, May 201

1, 2, 3, 4: Infusing Quantitative Literacy into Introductory Biology

Biology of the twenty-first century is an increasingly quantitative science. Undergraduate biology education therefore needs to provide opportunities for students to develop fluency in the tools and language of quantitative disciplines. Quantitative literacy (QL) is important for future scientists as well as for citizens, who need to interpret numeric information and data-based claims regarding nearly every aspect of daily life. To address the need for QL in biology education, we incorporated quantitative concepts throughout a semester-long introductory biology course at a large research university. Early in the course, we assessed the quantitative skills that students bring to the introductory biology classroom and found that students had difficulties in performing simple calculations, representing data graphically, and articulating data-driven arguments. In response to students' learning needs, we infused the course with quantitative concepts aligned with the existing course content and learning objectives. The effectiveness of this approach is demonstrated by significant improvement in the quality of students' graphical representations of biological data. Infusing QL in introductory biology presents challenges. Our study, however, supports the conclusion that it is feasible in the context of an existing course, consistent with the goals of college biology education, and promotes students' development of important quantitative skills

The Iceland Greenland Seas Project

A coordinated atmosphere-ocean research project, centered on a rare wintertime field campaign to the Iceland and Greenland Seas, seeks to determine the location and causes of dense water formation by cold-air outbreaks. The Iceland Greenland Seas Project (IGP) is a coordinated atmosphere-ocean research program investigating climate processes in the source region of the densest waters of the Atlantic Meridional Overturning Circulation. During February and March 2018, a field campaign was executed over the Iceland and southern Greenland Seas that utilized a range of observing platforms to investigate critical processes in the region – including a research vessel, a research aircraft, moorings, sea gliders, floats and a meteorological buoy. A remarkable feature of the field campaign was the highly-coordinated deployment of the observing platforms, whereby the research vessel and aircraft tracks were planned in concert to allow simultaneous sampling of the atmosphere, the ocean and their interactions. This joint planning was supported by tailor-made convection-permitting weather forecasts and novel diagnostics from an ensemble prediction system. The scientific aims of the IGP are to characterize the atmospheric forcing and the ocean response of coupled processes; in particular, cold-air outbreaks in the vicinity of the marginal-ice zone and their triggering of oceanic heat loss, and the role of freshwater in the generation of dense water masses. The campaign observed the lifecycle of a long-lasting cold-air outbreak over the Iceland Sea and the development of a cold-air outbreak over the Greenland Sea. Repeated profiling revealed the immediate impact on the ocean, while a comprehensive hydrographic survey provided a rare picture of these subpolar seas in winter. A joint atmosphere-ocean approach is also being used in the analysis phase, with coupled observational analysis and coordinated numerical modelling activities underway

A missense mutation in the MLKL brace region promotes lethal neonatal inflammation and hematopoietic dysfunction

MLKL is the essential effector of necroptosis, a form of programmed lytic cell death. We have isolated a mouse strain with a single missense mutation, Mlkl(D139V), that alters the two-helix 'brace' that connects the killer four-helix bundle and regulatory pseudokinase domains. This confers constitutive, RIPK3 independent killing activity to MLKL. Homozygous mutant mice develop lethal postnatal inflammation of the salivary glands and mediastinum. The normal embryonic development of Mlkl(D139V) homozygotes until birth, and the absence of any overt phenotype in heterozygotes provides important in vivo precedent for the capacity of cells to clear activated MLKL. These observations offer an important insight into the potential disease-modulating roles of three common human MLKL polymorphisms that encode amino acid substitutions within or adjacent to the brace region. Compound heterozygosity of these variants is found at up to 12-fold the expected frequency in patients that suffer from a pediatric autoinflammatory disease, chronic recurrent multifocal osteomyelitis (CRMO). Necroptosis is a regulated form of inflammatory cell death driven by activated MLKL. Here, the authors identify a mutation in the brace region that confers constitutive activation, leading to lethal inflammation in homozygous mutant mice and providing insight into human mutations in this region

Arginine Cofactors on the Polymerase Ribozyme

The RNA world hypothesis states that the early evolution of life went through a stage in which RNA served both as genome and as catalyst. The central catalyst in an RNA world organism would have been a ribozyme that catalyzed RNA polymerization to facilitate self-replication. An RNA polymerase ribozyme was developed previously in the lab but it is not efficient enough for self-replication. The factor that limits its polymerization efficiency is its weak sequence-independent binding of the primer/template substrate. Here we tested whether RNA polymerization could be improved by a cationic arginine cofactor, to improve the interaction with the substrate. In an RNA world, amino acid-nucleic acid conjugates could have facilitated the emergence of the translation apparatus and the transition to an RNP world. We chose the amino acid arginine for our study because this is the amino acid most adept to interact with RNA. An arginine cofactor was positioned at ten different sites on the ribozyme, using conjugates of arginine with short DNA or RNA oligonucleotides. However, polymerization efficiency was not increased in any of the ten positions. In five of the ten positions the arginine reduced or modulated polymerization efficiency, which gives insight into the substrate-binding site on the ribozyme. These results suggest that the existing polymerase ribozyme is not well suited to using an arginine cofactor