Effect of the Berendsen thermostat on dynamical properties of water

The effect of the Berendsen thermostat on the dynamical properties of bulk SPC/E water is tested by generating power spectra associated with fluctuations in various observables. The Berendsen thermostat is found to be very effective in preserving temporal correlations in fluctuations of tagged particle quantities over a very wide range of frequencies. Even correlations in fluctuations of global properties, such as the total potential energy, are well-preserved for time periods shorter than the thermostat time constant. Deviations in dynamical behaviour from the microcanonical limit do not, however, always decrease smoothly with increasing values of the thermostat time constant but may be somewhat larger for some intermediate values of $\tau_B$, specially in the supercooled regime, which are similar to time scales for slow relaxation processes in bulk water.Comment: 21 pages, 5 figures, To be published in Mol. Phy

Comparison of Different Boost Transformations for the Calculation of Form Factors in Relativistic Quantum Mechanics

The effect of different boost expressions, pertinent to the instant, front and point forms of relativistic quantum mechanics, is considered for the calculation of the ground-state form factor of a two-body system in simple scalar models. Results with a Galilean boost as well as an explicitly covariant calculation based on the Bethe-Salpeter approach are given for comparison. It is found that the present so-called point-form calculations of form factors strongly deviate from all the other ones. This suggests that the formalism which underlies them requires further elaboration. A proposition in this sense is made.Comment: Invited talk given at the 18th European Conference on Few-Body Problems in Physics, Bled, Slovenia, 8-14 Sep 2002. Submitted to Few Body Syst.Supp

Marine prasinoviruses and their tiny plankton hosts: A review

This is the final version. Available on open access from MDPI via the DOI in this recordViruses play a crucial role in the marine environment, promoting nutrient recycling and biogeochemical cycling and driving evolutionary processes. Tiny marine phytoplankton called prasinophytes are ubiquitous and significant contributors to global primary production and biomass. A number of viruses (known as prasinoviruses) that infect these important primary producers have been isolated and characterised over the past decade. Here we review the current body of knowledge about prasinoviruses and their interactions with their algal hosts. Several genes, including those encoding for glycosyltransferases, methyltransferases and amino acid synthesis enzymes, which have never been identified in viruses of eukaryotes previously, have been detected in prasinovirus genomes. The host organisms are also intriguing; most recently, an immunity chromosome used by a prasinophyte in response to viral infection was discovered. In light of such recent, novel discoveries, we discuss why the cellular simplicity of prasinophytes makes for appealing model host organism–virus systems to facilitate focused and detailed investigations into the dynamics of marine viruses and their intimate associations with host species. We encourage the adoption of the prasinophyte Ostreococcus and its associated viruses as a model host–virus system for examination of cellular and molecular processes in the marine environment

Looking back at superfluid helium

A few years after the discovery of Bose Einstein condensation in several gases, it is interesting to look back at some properties of superfluid helium. After a short historical review, I comment shortly on boiling and evaporation, then on the role of rotons and vortices in the existence of a critical velocity in superfluid helium. I finally discuss the existence of a condensate in a liquid with strong interactions, and the pressure variation of its superfluid transition temperature.Comment: Conference "Bose Einstein Condensation", Institut henri Poincare, Paris, 29 march 200

Fault Models for Quantum Mechanical Switching Networks

The difference between faults and errors is that, unlike faults, errors can be corrected using control codes. In classical test and verification one develops a test set separating a correct circuit from a circuit containing any considered fault. Classical faults are modelled at the logical level by fault models that act on classical states. The stuck fault model, thought of as a lead connected to a power rail or to a ground, is most typically considered. A classical test set complete for the stuck fault model propagates both binary basis states, 0 and 1, through all nodes in a network and is known to detect many physical faults. A classical test set complete for the stuck fault model allows all circuit nodes to be completely tested and verifies the function of many gates. It is natural to ask if one may adapt any of the known classical methods to test quantum circuits. Of course, classical fault models do not capture all the logical failures found in quantum circuits. The first obstacle faced when using methods from classical test is developing a set of realistic quantum-logical fault models. Developing fault models to abstract the test problem away from the device level motivated our study. Several results are established. First, we describe typical modes of failure present in the physical design of quantum circuits. From this we develop fault models for quantum binary circuits that enable testing at the logical level. The application of these fault models is shown by adapting the classical test set generation technique known as constructing a fault table to generate quantum test sets. A test set developed using this method is shown to detect each of the considered faults.Comment: (almost) Forgotten rewrite from 200

Changes in benthos following the clean-up of a severely metal-polluted cove in the Hudson River estuary: Environmental restoration or ecological disturbance?

We studied changes in macrobenthic communities following the environmental clean-up of metal-polluted (cadmium, nickel, and cobalt) sediments in Foundry Cove, a small inlet within the Hudson River estuary of New York. We used a BACI-style experiment to test the hypotheses that high levels of cadmium in sediments change macrobenthic assemblages relative to unpolluted areas, and removal of metals (especially cadmium) by dredging will restore the benthos, such that benthic fauna in Foundry Cove are not different from unpolluted areas. In 1984, prior to the restoration work, there were no significant differneces between macrobenthic assemblages in polluted and unpolluted locations, indicating that cadmium had little effect on community structure. The lack of an observed toxicity effect may have been caused by the compensatory evolution of resistance to cadmium in dominant organisms. Six years after the restoration work and despite a substantial reduction in metal pollution, there were lower abundances of oligochaetes, nematodes, and chironomids and a higher abundance of polychaetes at Foundry Cove relative to reference locations. Correlative analyses identified greater sediment compaction caused by dredging at Foundry, Cove as a possible cause of faunal differences

Measuring the symptomatic, physical, emotional and social impacts of dry mouth: A qualitative study

Objective To explore the impacts of dry mouth in order to develop a comprehensive condition‐specific OHRQoL measure. Background Dry mouth has been shown to have significant, if not more severe impacts on OHRQoL, than dental caries. Yet there remain few studies reporting on how to develop a comprehensive measure of the impact of dry mouth on OHRQoL. Methods This study was a qualitative study using semi‐structured interviews. Data were collected from a purposive sample of 17 people with dry mouth (14 women, three men). The sample was drawn to capture a comprehensive range of impacts of dry mouth. These interviews were analysed using a framework approach informed by existing functionalist approaches to OHRQoL. Results Participants reported a huge range of symptoms associated with perceived dry mouth resulting in extensive impacts on physical, emotional (psychological) and social functioning. Dry mouth could also result in restrictions in social participation which, under some conditions, could be disabling. These impacts were modified by psychological, social and environmental factors. Conclusions If we are to measure the impacts of oral conditions, it is important that this is done systematically and with reference to existing conceptual models of health. Current measures of the impact of dry mouth cover symptoms, discomfort and physical impacts along with some aspects of how people cope with the condition. This study proposes a more comprehensive approach that includes the full range of impacts people experience. Such an approach may enable us to focus on “downstream” and “upstream” interventions for dry mouth

An exact expression to calculate the derivatives of position-dependent observables in molecular simulations with flexible constraints

In this work, we introduce an algorithm to compute the derivatives of physical observables along the constrained subspace when flexible constraints are imposed on the system (i.e., constraints in which the hard coordinates are fixed to configuration-dependent values). The presented scheme is exact, it does not contain any tunable parameter, and it only requires the calculation and inversion of a sub-block of the Hessian matrix of second derivatives of the function through which the constraints are defined. We also present a practical application to the case in which the sought observables are the Euclidean coordinates of complex molecular systems, and the function whose minimization defines the constraints is the potential energy. Finally, and in order to validate the method, which, as far as we are aware, is the first of its kind in the literature, we compare it to the natural and straightforward finite-differences approach in three molecules of biological relevance: methanol, N-methyl-acetamide and a tri-glycine peptideComment: 13 pages, 8 figures, published versio

Plant–soil feedback of native and range-expanding plant species is insensitive to temperature

Temperature change affects many aboveground and belowground ecosystem processes. Here we investigate the effect of a 5°C temperature increase on plant–soil feedback. We compare plant species from a temperate climate region with immigrant plants that originate from warmer regions and have recently shifted their range polewards. We tested whether the magnitude of plant–soil feedback is affected by ambient temperature and whether the effect of temperature differs between these groups of plant species. Six European/Eurasian plant species that recently colonized the Netherlands (non-natives), and six related species (natives) from the Netherlands were selected. Plant–soil feedback of these species was determined by comparing performance in conspecific and heterospecific soils. In order to test the effect of temperature on these plant–soil feedback interactions, the experiments were performed at two greenhouse temperatures of 20/15°C and 25/20°C, respectively. Inoculation with unconditioned soil had the same effect on natives and non-natives. However, the effect of conspecific conditioned soil was negative compared to heterospecific soil for natives, but was positive for non-natives. In both cases, plant–soil interactions were not affected by temperature. Therefore, we conclude that the temperature component of climate change does not affect the direction, or strength of plant–soil feedback, neither for native nor for non-native plant species. However, as the non-natives have a more positive soil feedback than natives, climate warming may introduce new plant species in temperate regions that have less soil-borne control of abundance