Reactive Force Field for Proton Diffusion in BaZrO3 using an empirical valence bond approach

A new reactive force field to describe proton diffusion within the solid-oxide fuel cell material BaZrO3 has been derived. Using a quantum mechanical potential energy surface, the parameters of an interatomic potential model to describe hydroxyl groups within both pure and yttrium-doped BaZrO3 have been determined. Reactivity is then incorporated through the use of the empirical valence bond model. Molecular dynamics simulations (EVB-MD) have been performed to explore the diffusion of hydrogen using a stochastic thermostat and barostat whose equations are extended to the isostress-isothermal ensemble. In the low concentration limit, the presence of yttrium is found not to significantly influence the diffusivity of hydrogen, despite the proton having a longer residence time at oxygen adjacent to the dopant. This lack of influence is due to the fact that trapping occurs infrequently, even when the proton diffuses through octahedra adjacent to the dopant. The activation energy for diffusion is found to be 0.42 eV, in good agreement with experimental values, though the prefactor is slightly underestimated.Comment: Corrected titl

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

We present a method for determining the free energy dependence on a selected number of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled. The parameters of the simulation can be tuned so as to focus the computational effort only on the physically relevant regions of the order parameter space. The algorithm is tested on the reconstruction of alanine dipeptide free energy landscape

Modelling the future impacts of climate and land-use change on suspended sediment transport in the River Thames (UK)

The effects of climate change and variability on river flows have been widely studied. However the impacts of such changes on sediment transport have received comparatively little attention. In part this is because modelling sediment production and transport processes introduces additional uncertainty, but it also results from the fact that, alongside the climate change signal, there have been and are projected to be significant changes in land cover which strongly affect sediment-related processes. Here we assess the impact of a range of climatic variations and land covers on the River Thames catchment (UK). We first calculate a response of the system to climatic stressors (average precipitation, average temperature and increase in extreme precipitation) and land-cover stressors (change in the extent of arable land). To do this we use an ensemble of INCA hydrological and sediment behavioural models. The resulting system response, which reveals the nature of interactions between the driving factors, is then compared with climate projections originating from the UKCP09 assessment (UK Climate Projections 2009) to evaluate the likelihood of the range of projected outcomes. The results show that climate and land cover each exert an individual control on sediment transport. Their effects vary depending on the land use and on the level of projected climate change. The suspended sediment yield of the River Thames in its lowermost reach is expected to change by −4% (−16% to +13%, confidence interval, p = 0.95) under the A1FI emission scenario for the 2030s, although these figures could be substantially altered by an increase in extreme precipitation, which could raise the suspended sediment yield up to an additional +10%. A 70% increase in the extension of the arable land is projected to increase sediment yield by around 12% in the lowland reaches. A 50% reduction is projected to decrease sediment yield by around 13%

Colored-noise thermostats \`a la carte

Recently, we have shown how a colored-noise Langevin equation can be used in the context of molecular dynamics as a tool to obtain dynamical trajectories whose properties are tailored to display desired sampling features. In the present paper, after having reviewed some analytical results for the stochastic differential equations forming the basis of our approach, we describe in detail the implementation of the generalized Langevin equation thermostat and the fitting procedure used to obtain optimal parameters. We discuss in detail the simulation of nuclear quantum effects, and demonstrate that, by carefully choosing parameters, one can successfully model strongly anharmonic solids such as neon. For the reader's convenience, a library of thermostat parameters and some demonstrative code can be downloaded from an on-line repository

Fitting Corrections to an RNA Force Field Using Experimental Data

Empirical force fields for biomolecular systems are usually derived from quantum chemistry calculations and validated against experimental data. We here show how it is possible to refine the full dihedral-angle potential of the Amber RNA force field by using solution NMR data as well as stability of known structural motifs. The procedure can be used to mix multiple systems and heterogeneous experimental information and crucially depends on a regularization term chosen with a cross-validation procedure. By fitting corrections to the dihedral angles on the order of less than 1 kJ/mol per angle, it is possible to increase the stability of difficult-to-fold RNA tetraloops by more than 1 order of magnitude

Dynamic response of land use and river nutrient concentration to long-term climatic changes

The combined indirect and direct impacts of land use change and climate change on river water quality were assessed. A land use allocation model was used to evaluate the response of the catchment land use to long-term climatic changes. Its results were used to drive a water quality model and assess the impact of climatic alterations on freshwater nitrate and phosphorus concentrations. Climatic projections were employed to estimate the likelihood of such response. The River Thames catchment (UK) was used as a case-study. If land use is considered as static parameter, according to the model results, climate change alone should reduce the average nitrate concentration, although just by a small amount, by the 2050s in the Lower Thames, due to reduced runoff (and lower export of nitrate from agricultural soils) and increased instream denitrification, and should increase the average phosphorus concentration by 12% by the 2050s in the Lower Thames, due to a reduction of the effluent dilution capacity of the river flow. However, the results of this study also show that these long-term climatic alterations are likely to lead to a reduction in the arable land in the Thames, replaced by improved grassland, due to a decrease in agriculture profitability in the UK. Taking into account the dynamic co-evolution of land use with climate, the average nitrate concentration is expected to be decreased by around 6% by the 2050s in both the upper and the lower Thames, following the model results, and the average phosphorus concentration increased by 13% in the upper Thames and 5% in the lower Thames. On the long term (2080s), nitrate is expected to decrease by 9% and 8% (upper and lower Thames respectively) and phosphorus not to change in the upper thames and increase by 5% in the lower Thames

Assessment of risks to public water supply from low flows and harmful water quality in a changing climate

Water resources planning and management by water utilities have traditionally been based on consideration of water availability. However, the reliability of public water supplies can also be influenced by the quality of water bodies. In this study, we proposed a framework that integrates the analysis of risks of inadequate water quality and risks of insufficient water availability. We have developed a coupled modeling system that combines hydrological modeling of river water quantity and quality, rules for water withdrawals from rivers into storage reservoirs, and dynamical simulation of harmful algal blooms in storage reservoirs. We use this framework to assess the impact of climate change, demand growth, and land‐use change on the reliability of public water supplies. The proposed method is tested on the River Thames catchment in the south of England. The results show that alongside the well‐known risks of rising water demand in the south of England and uncertain impacts of climate change, diffuse pollution from agriculture and effluent from upstream waste water treatment works potentially represent a threat to the reliability of public water supplies in London. We quantify the steps that could be taken to ameliorate these threats, though even a vigorous pollution‐prevention strategy would not be sufficient to offset the projected effects of climate change on water quality and the reliability of public water supplies. The proposed method can help water utilities to recognize their system vulnerability and evaluate the potential solutions to achieve more reliable water supplies. supplie

Interchain interaction and Davydov splitting in polythiophene crystals: An ab initio approach

The crystal-induced energy splitting of the lowest excitonic state in polymer crystals, the so-called Davydov splitting Δ, is calculated with a first-principles density-matrix scheme. We show that different crystalline arrangements lead to significant variations in Δ, from below to above the thermal energy kBT at room temperature, with relevant implications on the luminescence efficiency. This is one more piece of evidence supporting the fact that control of interchain interactions and solid-state packing is essential for the design of efficient optical devices

Asymmetric base-pair opening drives helicase unwinding dynamics

The opening of a Watson-Crick double helix is required for crucial cellular processes, including replication, repair, and transcription. It has long been assumed that RNA or DNA base pairs are broken by the concerted symmetric movement of complementary nucleobases. By analyzing thousands of base-pair opening and closing events from molecular simulations, here, we uncover a systematic stepwise process driven by the asymmetric flipping-out probability of paired nucleobases. We demonstrate experimentally that such asymmetry strongly biases the unwinding efficiency of DNA helicases toward substrates that bear highly dynamic nucleobases, such as pyrimidines, on the displaced strand. Duplex substrates with identical thermodynamic stability are thus shown to be more easily unwound from one side than the other, in a quantifiable and predictable manner. Our results indicate a possible layer of gene regulation coded in the direction-dependent unwindability of the double helix

Quantum Interferences in the Raman Cross Section for the Radial Breathing Mode in Metalic Carbon Nanotubes

The lineshapes of the Raman excitation profiles for radial breathing modes in carbon nanotubes are shown to be strongly affected by interference effects that arise whenever strong optical transitions are separated by a small energy. This is the case in metallic zigzag and chiral tubes, where one-dimensional singularities in the electronic joint density of states are split due to the trigonal warping of the electronic band structure of two-dimensional graphene. It is shown that the proper modeling of these interferences is crucial for the identification of the (n,m) indices using Raman spectroscopy.Comment: 10 pages, 3 figure