The sign problem and population dynamics in the full configuration interaction quantum Monte Carlo method

The recently proposed full configuration interaction quantum Monte Carlo method allows access to essentially exact ground-state energies of systems of interacting fermions substantially larger than previously tractable without knowledge of the nodal structure of the ground-state wave function. We investigate the nature of the sign problem in this method and how its severity depends on the system studied. We explain how cancelation of the positive and negative particles sampling the wave function ensures convergence to a stochastic representation of the many-fermion ground state and accounts for the characteristic population dynamics observed in simulations.Comment: 11 pages. 6 figure

Developmental stage-specific regulation of the circadian Clock by Temperature in Zebrafish

The circadian clock enables animals to adapt their physiology and behaviour in anticipation of the day-night cycle. Light and temperature represent two key environmental timing cues (zeitgebers) able to reset this mechanism and so maintain its synchronization with the environmental cycle. One key challenge is to unravel how the regulation of the clock by zeitgebers matures during early development. The zebrafish is an ideal model for studying circadian clock ontogeny since the process of development occurs ex utero in an optically transparent chorion and many tools are available for genetic analysis. However, the role played by temperature in regulating the clock during zebrafish development is poorly understood. Here, we have established a clock-regulated luciferase reporter transgenic zebrafish line (Tg (−3.1) per1b::luc) to study the effects of temperature on clock entrainment. We reveal that under complete darkness, from an early developmental stage onwards (48 to 72 hpf), exposure to temperature cycles is a prerequisite for the establishment of self-sustaining rhythms of zfper1b, zfaanat2, and zfirbp expression and also for circadian cell cycle rhythms. Furthermore, we show that following the 5–9 somite stage, the expression of zfper1b is regulated by acute temperature shifts

Accurate exchange-correlation energies for the warm dense electron gas

Density matrix quantum Monte Carlo (DMQMC) is used to sample exact-on-average $N$-body density matrices for uniform electron gas systems of up to 10$^{124}$ matrix elements via a stochastic solution of the Bloch equation. The results of these calculations resolve a current debate over the accuracy of the data used to parametrize finite-temperature density functionals. Exchange-correlation energies calculated using the real-space restricted path-integral formalism and the $k$-space configuration path-integral formalism disagree by up to $\sim$$10$\% at certain reduced temperatures $T/T_F \le 0.5$ and densities $r_s \le 1$. Our calculations confirm the accuracy of the configuration path-integral Monte Carlo results available at high density and bridge the gap to lower densities, providing trustworthy data in the regime typical of planetary interiors and solids subject to laser irradiation. We demonstrate that DMQMC can calculate free energies directly and present exact free energies for $T/T_F \ge 1$ and $r_s \le 2$.Comment: Accepted version: added free energy data and restructured text. Now includes supplementary materia

Open-source development experiences in scientific software: the HANDE quantum Monte Carlo project

The HANDE quantum Monte Carlo project offers accessible stochastic algorithms for general use for scientists in the field of quantum chemistry. HANDE is an ambitious and general high-performance code developed by a geographically-dispersed team with a variety of backgrounds in computational science. In the course of preparing a public, open-source release, we have taken this opportunity to step back and look at what we have done and what we hope to do in the future. We pay particular attention to development processes, the approach taken to train students joining the project, and how a flat hierarchical structure aids communicationComment: 6 pages. Submission to WSSSPE

Tolerance of septoria leaf blotch in winter wheat

For individual varieties, tolerance of septoria leaf blotch was quantified by the slope of the relationship between disease and yield. Variation in disease severity and the associated yield responses were provided across two sites and three seasons of field experiments. Slopes were fitted by residual maximum likelihood for two contrasting models: (i) a fixed-effects model, where no prior assumptions were made about the form of the variety slopes; and (ii) a random-effects model, where deviations in individual variety slopes away from the mean variety slope formed a normal random population with unknown variance. The analyses gave broadly similar results, but with some significant differences. The random model was considered more reliable for predicting variety performance. The effects of disease were quantified as symptom area and green canopy duration. Models of the relationship between symptom area and yield were site-specific. When site effects were not taken into account, these models had poor predictive precision. Models based on the canopy green area gave robust predictions of yield and were not site-specific. Differences in disease tolerance were detected in a comparison of 25 commercial winter wheat varieties. Tolerance was not detected directly through symptom measurements, but instead through measurements of canopy green area, which provides a measurement of the effects of disease that accounts for differences in canopy size across sites and seasons. The varieties showing greatest tolerance tended to have lower attainable yield than the intolerant varieties. Presence of the 1BL/1RS chromosome translocation, which has been reported to increase radiation use efficiency, appeared to be associated with intolerance

Mutations in blind cavefish target the light-regulated circadian clock gene, period 2

Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors

Riding a Spiral Wave: Numerical Simulation of Spiral Waves in a Co-Moving Frame of Reference

We describe an approach to numerical simulation of spiral waves dynamics of large spatial extent, using small computational grids.Comment: 15 pages, 14 figures, as accepted by Phys Rev E 2010/03/2

YB-1 recruitment to stress granules in zebrafish cells reveals a differential adaptive response to stress

The survival of cells exposed to adverse environmental conditions entails various alterations in cellular function including major changes in the transcriptome as well as a radical reprogramming of protein translation. While in mammals this process has been extensively studied, stress responses in non-mammalian vertebrates remain poorly understood. One of the key cellular responses to many different types of stressors is the transient generation of structures called stress granules (SGs). These represent cytoplasmic foci where untranslated mRNAs are sorted or processed for re-initiation, degradation, or packaging into mRNPs. Here, using the evolutionarily conserved Y-box binding protein 1 (YB-1) and G3BP1 as markers, we have studied the formation of stress granules in zebrafish (D. rerio) in response to different environmental stressors. We show that following heat shock, zebrafish cells, like mammalian cells, form stress granules which contain both YB-1 and G3BP1 proteins. Moreover, zfYB-1 knockdown compromises cell viability, as well as recruitment of G3BP1 into SGs, under heat shock conditions highlighting the essential role played by YB-1 in SG assembly and cell survival. However, zebrafish PAC2 cells do not assemble YB-1-positive stress granules upon oxidative stress induced by arsenite, copper or hydrogen peroxide treatment. This contrasts with the situation in human cells where SG formation is robustly induced by exposure to oxidative stressors. Thus, our findings point to fundamental differences in the mechanisms whereby mammalian and zebrafish cells respond to oxidative stress

Variational quantum Monte Carlo calculations for solid surfaces

Quantum Monte Carlo methods have proven to predict atomic and bulk properties of light and non-light elements with high accuracy. Here we report on the first variational quantum Monte Carlo (VMC) calculations for solid surfaces. Taking the boundary condition for the simulation from a finite layer geometry, the Hamiltonian, including a nonlocal pseudopotential, is cast in a layer resolved form and evaluated with a two-dimensional Ewald summation technique. The exact cancellation of all Jellium contributions to the Hamiltonian is ensured. The many-body trial wave function consists of a Slater determinant with parameterized localized orbitals and a Jastrow factor with a common two-body term plus a new confinement term representing further variational freedom to take into account the existence of the surface. We present results for the ideal (110) surface of Galliumarsenide for different system sizes. With the optimized trial wave function, we determine some properties related to a solid surface to illustrate that VMC techniques provide standard results under full inclusion of many-body effects at solid surfaces.Comment: 9 pages with 2 figures (eps) included, Latex 2.09, uses REVTEX style, submitted to Phys. Rev.