Ramachandran-type Plots for Glycosidic Linkages: Examples from Molecular Dynamics Simulations using the Glycam06 Force Field

The goals of this article are to (1) provide further validation of the Glycam06 force field, specifically for its use in implicit solvent molecular dynamic (MD) simulations, and (2) to present the extension of G.N. Ramachandran's idea of plotting amino acid phi and psi angles to the glycosidic phi, psi, and omega angles formed between carbohydrates. As in traditional Ramachandran plots, these carbohydrate Ramachandran-type (carb-Rama) plots reveal the coupling between the glycosidic angles by displaying the allowed and disallowed conformational space. Considering two-bond glycosidic linkages, there are 18 possible conformational regions that can be defined by (α, ϕ, ψ) and (β, ϕ, ψ), whereas for three-bond linkages, there are 54 possible regions that can be defined by (α, ϕ, ψ, ω) and (β, ϕ, ψ, ω). Illustrating these ideas are molecular dynamic simulations on an implicitly hydrated oligosaccharide (700 ns) and its eight constituent disaccharides (50 ns/disaccharide). For each linkage, we compare and contrast the oligosaccharide and respective disaccharide carb-Rama plots, validate the simulations and the Glycam06 force field through comparison to experimental data, and discuss the general trends observed in the plots.

No adverse effect of genetically modified antifungal wheat on decomposition dynamics and the soil fauna community - a field study

The cultivation of genetically modified (GM) plants has raised several environmental concerns. One of these concerns regards non-target soil fauna organisms, which play an important role in the decomposition of organic matter and hence are largely exposed to GM plant residues. Soil fauna may be directly affected by transgene products or indirectly by pleiotropic effects such as a modified plant metabolism. Thus, ecosystem services and functioning might be affected negatively. In a litterbag experiment in the field we analysed the decomposition process and the soil fauna community involved. Therefore, we used four experimental GM wheat varieties, two with a race-specific antifungal resistance against powdery mildew (Pm3b) and two with an unspecific antifungal resistance based on the expression of chitinase and glucanase. We compared them with two non-GM isolines and six conventional cereal varieties. To elucidate the mechanisms that cause differences in plant decomposition, structural plant components (i.e. C:N ratio, lignin, cellulose, hemicellulose) were examined and soil properties, temperature and precipitation were monitored. The most frequent taxa extracted from decaying plant material were mites (Cryptostigmata, Gamasina and Uropodina), springtails (Isotomidae), annelids (Enchytraeidae) and Diptera (Cecidomyiidae larvae). Despite a single significant transgenic/month interaction for Cecidomyiidae larvae, which is probably random, we detected no impact of the GM wheat on the soil fauna community. However, soil fauna differences among conventional cereal varieties were more pronounced than between GM and non-GM wheat. While leaf residue decomposition in GM and non-GM wheat was similar, differences among conventional cereals were evident. Furthermore, sampling date and location were found to greatly influence soil fauna community and decomposition processes. The results give no indication of ecologically relevant adverse effects of antifungal GM wheat on the composition and the activity of the soil fauna community.

Dynamics in the governance of collective irrigation systems: Evidence from field experiments in Nicaragua.

In this paper, we investigate the real demand for climate protection when the purely individual perspective of existing revealed preference studies is relaxed. This is achieved in two treatments; first, we determine the information subjects receive about the demand revealed by other subjects in a similar decision making situation, second, collective action is implemented whereby all subjects are required to purchase the group?s median quantity at a given price. Participants in the experiment were offered the opportunity to contribute to climate protection by purchasing European Union Allowances. Allowances purchased were withdrawn from the European Emissions Trading Scheme. In our experiment, information about other subjects? behaviour has no treatment effect on the demand for climate protection. Under collective action however, the probability of purchasing allowances is higher compared to the reference treatment situation, an individual contribution mechanism. Furthermore, we observe a strong correlation between subjects? demand and their expectations about other participants? behaviour. When collective action is not available, subjects? e xpectations are consistent with free rider behaviour.

Dynamics in the governance of collective irrigation systems: Evidence from field experiments in Nicaragua.

The objective of this study is to analyze the common pool resource appropriation and public good provisiondecisions in a dynamic setting, testing the differences in behavior and performance between lab and field subjects. We performeda total of 45 games in Nicaragua, including 88 villagers in rural communities and 92 undergraduate students. In order to analyze sequential decision making, we introduce a dynamic and asymmetric irrigation game that combines the typical social dilemmas associated to irrigation systems management.In addition, in 9 out of 22 villagers’ groups, we implemented a treatment that included the disclosure of subjects’ appropriation of the common pool resource. The results reveal that the provision of individuals’ appropriation level results in higher appropriation in subsequent rounds. In addition, the results show that non-treated villagers provide more public good than treated villagers but if compared with students the differences are not significant. The results also suggest that appropriation levels are below the Nash prediction of full appropriation, but above the social efficient level. This results in an efficiency loss in the game that can be explained to a large extent by individual decisions on appropriation and public good contribution and by group appropriation behavior.

Molecular dynamics of a grid-mounted molecular dipolar rotor in a rotating electric field

Classical molecular dynamics is applied to the rotation of a dipolar molecular rotor mounted on a square grid and driven by rotating electric field E(ν) at T ≃ 150 K. The rotor is a complex of Re with two substituted o-phenanthrolines, one positively and one negatively charged, attached to an axial position of Rh\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{2}^{4+}}}\end{equation*}\end{document} in a [2]staffanedicarboxylate grid through 2-(3-cyanobicyclo[1.1.1]pent-1-yl)malonic dialdehyde. Four regimes are characterized by a, the average lag per turn: (i) synchronous (a < 1/e) at E(ν) = |E(ν)| > Ec(ν) [Ec(ν) is the critical field strength], (ii) asynchronous (1/e < a < 1) at Ec(ν) > E(ν) > Ebo(ν) > kT/μ, [Ebo(ν) is the break-off field strength], (iii) random driven (a ≃ 1) at Ebo(ν) > E(ν) > kT/μ, and (iv) random thermal (a ≃ 1) at kT/μ > E(ν). A fifth regime, (v) strongly hindered, W > kT, Eμ, (W is the rotational barrier), has not been examined. We find Ebo(ν)/kVcm−1 ≃ (kT/μ)/kVcm−1 + 0.13(ν/GHz)1.9 and Ec(ν)/kVcm−1 ≃ (2.3kT/μ)/kVcm−1 + 0.87(ν/GHz)1.6. For ν > 40 GHz, the rotor behaves as a macroscopic body with a friction constant proportional to frequency, η/eVps ≃ 1.14 ν/THz, and for ν < 20 GHz, it exhibits a uniquely molecular behavior.

Nonequilibrium spin glass dynamics with Janus

The out of equilibrium evolution for an Edwards‐Anderson spin glass is followed for a tenth of a second, a long enough time to let us make safe predictions about the behaviour at experimental scales. This work has been made possible by Janus, an FPGA based special purpose computer. We have thoroughly studied the spin glass correlation functions and the growth of the coherence length for L = 80 lattices in 3D. Our main conclusion is that these spin glasses follow noncoarsening dynamics, at least up to the experimentally relevant time scales.

Nonequilibrium spin-glass dynamics from picoseconds to a tenth of a second

We study numerically the nonequilibrium dynamics of the Ising spin glass, for a time spanning 11 orders of magnitude, thus approaching the experimentally relevant scale (i.e., seconds). We introduce novel analysis techniques to compute the coherence length in a model-independent way. We present strong evidence for a replicon correlator and for overlap equivalence. The emerging picture is compatible with noncoarsening behavior.

Adiabatic approximation for dynamics of a particle in the field of a tapered solenoid /

"AEC Contract AT(04-3)-400."

Dynamics of loads on power systems using field measurements /

"May 1984."

Generalized mean field approximation for parallel dynamics of the Ising model

The dynamics of the non-equilibrium Ising model with parallel updates is investigated using a generalized mean field approximation that incorporates multiple two-site correlations at any two time steps, which can be obtained recursively. The proposed method shows significant improvement in predicting local system properties compared to other mean field approximation techniques, particularly in systems with symmetric interactions. Results are also evaluated against those obtained from Monte Carlo simulations. The method is also employed to obtain parameter values for the kinetic inverse Ising modeling problem, where couplings and local field values of a fully connected spin system are inferred from data. © 2014 IOP Publishing Ltd and SISSA Medialab srl.

Retrieval of implicit inhibitory processes:the impact of visual field, object-identity, and memory dynamics

After exogenously cueing attention to a peripheral location, the return of attention and response to the location can be inhibited. We demonstrate that these inhibitory mechanisms of attention can be associated with objects and can be automatically and implicitly retrieved over relatively long periods. Furthermore, we also show that when face stimuli are associated with inhibition, the effect is more robust for faces presented in the left visual field. This effect can be even more spatially specific, where most robust inhibition is obtained for faces presented in the upper as compared to the lower visual field. Finally, it is revealed that the inhibition is associated with an object’s identity, as inhibition moves with an object to a new location; and that the retrieved inhibition is only transiently present after retrieval.