Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1)

Challenges related to development, deployment, and maintenance of reusable software for science are becoming a growing concern. Many scientists’ research increasingly depends on the quality and availability of software upon which their works are built. To highlight some of these issues and share experiences, the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1) was held in November 2013 in conjunction with the SC13 Conference. The workshop featured keynote presentations and a large number (54) of solicited extended abstracts that were grouped into three themes and presented via panels. A set of collaborative notes of the presentations and discussion was taken during the workshop. Unique perspectives were captured about issues such as comprehensive documentation, development and deployment practices, software licenses and career paths for developers. Attribution systems that account for evidence of software contribution and impact were also discussed. These include mechanisms such as Digital Object Identifiers, publication of “software papers”, and the use of online systems, for example source code repositories like GitHub. This paper summarizes the issues and shared experiences that were discussed, including cross-cutting issues and use cases. It joins a nascent literature seeking to understand what drives software work in science, and how it is impacted by the reward systems of science. These incentives can determine the extent to which developers are motivated to build software for the long-term, for the use of others, and whether to work collaboratively or separately. It also explores community building, leadership, and dynamics in relation to successful scientific software

Plant virus infections control stomatal development

Stomata are important regulators of carbon dioxide uptake and transpirational water loss. They also represent points of vulnerability as bacterial and fungal pathogens utilise this natural opening as an entry portal, and thus have an increasingly complex relationship. Unlike the situation with bacterial and fungal pathogens, we know very little about the role of stomata in viral infection. Here we report findings showing that viral infection influences stomatal development in two susceptible host systems (Nicotiana tabacum with TMV (Tobacco mosaic virus), and Arabidopsis thaliana with TVCV (Turnip vein-clearing virus)), but not in resistant host systems (Nicotiana glutinosa and Chenopodium quinoa with TMV). Virus infected plants had significantly lower stomatal indices in systemic leaves of susceptible systems; N. tabacum 9.8% reduction and A. thaliana 12.3% reduction, but not in the resistant hosts. Stomatal density in systemic leaves was also significantly reduced in virus infected A. thaliana by 19.6% but not in N. tabacum or the resistant systems. In addition, transpiration rate was significantly reduced in TMV infected N. tabacum

Surveyor batteries Final engineering report

Design and performance of Surveyor spacecraft silver-zinc main batter

Testing the durability of limestone for Cathedral façade restoration

This research aimed to specify an optimum replacement stone for Truro Cathedral. A variety of petrographically and visually similar material to the original Bath stone was initially selected. The stones were subjected to three different durability tests; Sodium sulphate crystallisation and large scale testing with both accelerated and climatic freeze-thaw cyclic loading. The most suitable stone was determined as the one with the best performance characteristics overall

Exact Monte Carlo time dynamics in many-body lattice quantum systems

On the base of a Feynman-Kac--type formula involving Poisson stochastic processes, recently a Monte Carlo algorithm has been introduced, which describes exactly the real- or imaginary-time evolution of many-body lattice quantum systems. We extend this algorithm to the exact simulation of time-dependent correlation functions. The techniques generally employed in Monte Carlo simulations to control fluctuations, namely reconfigurations and importance sampling, are adapted to the present algorithm and their validity is rigorously proved. We complete the analysis by several examples for the hard-core boson Hubbard model and for the Heisenberg model

Random walks near Rokhsar-Kivelson points

There is a class of quantum Hamiltonians known as Rokhsar-Kivelson(RK)-Hamiltonians for which static ground state properties can be obtained by evaluating thermal expectation values for classical models. The ground state of an RK-Hamiltonian is known explicitly, and its dynamical properties can be obtained by performing a classical Monte Carlo simulation. We discuss the details of a Diffusion Monte Carlo method that is a good tool for studying statics and dynamics of perturbed RK-Hamiltonians without time discretization errors. As a general result we point out that the relation between the quantum dynamics and classical Monte Carlo simulations for RK-Hamiltonians follows from the known fact that the imaginary-time evolution operator that describes optimal importance sampling, in which the exact ground state is used as guiding function, is Markovian. Thus quantum dynamics can be studied by a classical Monte Carlo simulation for any Hamiltonian that is free of the sign problem provided its ground state is known explicitly.Comment: 12 pages, 9 figures, RevTe

Semiclassical description of spin ladders

The Heisenberg spin ladder is studied in the semiclassical limit, via a mapping to the nonlinear $\sigma$ model. Different treatments are needed if the inter-chain coupling $K$ is small, intermediate or large. For intermediate coupling a single nonlinear $\sigma$ model is used for the ladder. Its predicts a spin gap for all nonzero values of $K$ if the sum $s+\tilde s$ of the spins of the two chains is an integer, and no gap otherwise. For small $K$, a better treatment proceeds by coupling two nonlinear sigma models, one for each chain. For integer $s=\tilde s$, the saddle-point approximation predicts a sharp drop in the gap as $K$ increases from zero. A Monte-Carlo simulation of a spin 1 ladder is presented which supports the analytical results.Comment: 8 pages, RevTeX 3.0, 4 PostScript figure

Conditional citizens? welfare rights and responsibilities in the late 1990s

In Britain the relationship between welfare rights and responsibilities has undergone change. A new welfare 'consensus' that emphasizes a citizen ship centred on notions of duty rather than rights has been built. This has allowed the state to reduce its role as a provider of welfare and also defend a position in which the welfare rights of some citizens are increas ingly conditional on those individuals meeting compulsory responsibili ties or duties. This concentration on individual responsibility/duty has undermined the welfare rights of some of the poorest members of society. Three levels of debate are considered within the article: academic, pol itical and 'grassroots'. The latter is included in an attempt to allow some 'bottom up' views into what is largely a debate dominated by social sci entists and politicians

Optimization of ground and excited state wavefunctions and van der Waals clusters

A quantum Monte Carlo method is introduced to optimize excited state trial wavefunctions. The method is applied in a correlation function Monte Carlo calculation to compute ground and excited state energies of bosonic van der Waals clusters of upto seven particles. The calculations are performed using trial wavefunctions with general three-body correlations

Green Function Monte Carlo with Stochastic Reconfiguration: an effective remedy for the sign problem disease

A recent technique, proposed to alleviate the ``sign problem disease'', is discussed in details. As well known the ground state of a given Hamiltonian $H$ can be obtained by applying the imaginary time propagator $e^{-H \tau}$ to a given trial state $\psi_T$ for large imaginary time $\tau$ and sampling statistically the propagated state $\psi_{\tau} = e^{-H \tau} \psi_T$. However the so called ``sign problem'' may appear in the simulation and such statistical propagation would be practically impossible without employing some approximation such as the well known ``fixed node'' approximation (FN). This method allows to improve the FN dynamic with a systematic correction scheme. This is possible by the simple requirement that, after a short imaginary time propagation via the FN dynamic, a number $p$ of correlation functions can be further constrained to be {\em exact} by small perturbation of the FN propagated state, which is free of the sign problem. By iterating this scheme the Monte Carlo average sign, which is almost zero when there is sign problem, remains stable and finite even for large $\tau$. The proposed algorithm is tested against the exact diagonalization results available on finite lattice. It is also shown in few test cases that the dependence of the results upon the few parameters entering the stochastic technique can be very easily controlled, unless for exceptional cases.Comment: 44 pages, RevTeX + 5 encaplulated postscript figure