Statistical mechanical properties of sequence space determine the efficiency of the various algorithms to predict interaction energies and native contacts from protein coevolution.

Studying evolutionary correlations in alignments of homologous sequences by means of an inverse Potts model has proven useful to obtain residue-residue contact energies and to predict contacts in proteins. The quality of the results depend much on several choices of the detailed model and on the algorithms used. We built, in a very controlled way, synthetic alignments with statistical properties similar to those of real proteins, and used them to assess the performance of different inversion algorithms and of their variants. Realistic synthetic alignments display typical features of low-temperature phases of disordered systems, a feature that affects the inversion algorithms. We showed that a Boltzmann-learning algorithm is computationally feasible and performs well in predicting the energy of native contacts. However, all algorithms, when applied to alignments of realistic size, suffer of false positives quite equally, making the quality of the prediction of native contacts with the different algorithm much system-dependent.

Water quality modelling of the Mekong River basin: Climate change and socioeconomics drive flow and nutrient flux changes to the Mekong Delta.

The Mekong delta is recognised as one of the world's most vulnerable mega-deltas, being subject to a range of environmental pressures including sea level rise, increasing population, and changes in flows and nutrients from its upland catchment. With changing climate and socioeconomics there is a need to assess how the Mekong catchment will be affected in terms of the delivery of water and nutrients into the delta system. Here we apply the Integrated Catchment model (INCA) to the whole Mekong River Basin to simulate flow and water quality, including nitrate, ammonia, total phosphorus and soluble reactive phosphorus. The impacts of climate change on all these variables have been assessed across 24 river reaches ranging from the Himalayas down to the delta in Vietnam. We used the UK Met Office PRECIS regionally coupled climate model to downscale precipitation and temperature to the Mekong catchment. This was accomplished using the Global Circulation Model GFDL-CM to provide the boundary conditions under two carbon control strategies, namely representative concentration pathways (RCP) 4.5 and a RCP 8.5 scenario. The RCP 4.5 scenario represents the carbon strategy required to meet the Paris Accord, which aims to limit peak global temperatures to below a 2 °C rise whilst seeking to pursue options that limit temperature rise to 1.5 °C. The RCP 8.5 scenario is associated with a larger 3-4 °C rise. In addition, we also constructed a range of socio-economic scenarios to investigate the potential impacts of changing population, atmospheric pollution, economic growth and land use change up to the 2050s. Results of INCA simulations indicate increases in mean flows of up to 24%, with flood flows in the monsoon period increasing by up to 27%, but with increasing periods of drought up to 2050. A shift in the timing of the monsoon is also simulated, with a 4 week advance in the onset of monsoon flows on average. Decreases in nitrogen and phosphorus concentrations occur primarily due to flow dilution, but fluxes of these nutrients also increase by 5%, which reflects the changing flow, land use change and population changes.

Modelling heavy metals in the Buriganga River System, Dhaka, Bangladesh: Impacts of tannery pollution control.

Heavy metal pollution from tanneries is a global problem in many rapidly developing economies. Effluent discharges into rivers cause serious problems for water quality, damaging ecology and threatening the livelihoods of people, especially in developing urban centres which often have a high concentration of factories. The industry intensive capital area of Bangladesh is impacted with high levels of metals pollution in rivers in the Greater Dhaka Watershed. Sampling and modelling studies have been undertaken to assess pollution in the Buriganga River System in Dhaka. The process based, dynamic model INCA (Integrated Catchments) model has been used to simulate metals along the Buriganga River System in Central Dhaka. Observed and simulated metals concentrations are high, and the model shows that the proposed transfer of the tannery industry upstream helps to reduce the pollution significantly downstream. However, moving the industry upstream may be counterproductive as it is discharged into the upper reaches of the river. This will create pollution upstream unless the newly constructed effluent treatment system can operate at a high level.

Modelling metaldehyde in catchments: a River Thames case-study.

The application of metaldehyde to agricultural catchment areas to control slugs and snails has caused severe problems for drinking water supply in recent years. In the River Thames catchment, metaldehyde has been detected at levels well above the EU and UK drinking water standards of 0.1 µg l-1 at many sites across the catchment between 2008 and 2015. Metaldehyde is applied in autumn and winter, leading to its increased concentrations in surface waters. It is shown that a process-based hydro-biogeochemical transport model (INCA-contaminants) can be used to simulate metaldehyde transport in catchments from areas of application to the aquatic environment. Simulations indicate that high concentrations in the river system are a direct consequence of excessive application rates. A simple application control strategy for metaldehyde in the Thames catchment based on model results is presented.

Fate and transport of polychlorinated biphenyls (PCBs) in the River Thames catchment - Insights from a coupled multimedia fate and hydrobiogeochemical transport model.

The fate of persistent organic pollutants (POPs) in riverine environments is strongly influenced by hydrology (including flooding) and fluxes of sediments and organic carbon. Coupling multimedia fate models (MMFMs) and hydrobiogeochemical transport models offers unique opportunities for understanding the environmental behaviour of POPs. While MMFMs are widely used for simulating the fate and transport of legacy and emerging pollutants, they use greatly simplified representations of climate, hydrology and biogeochemical processes. Using additional information about weather, river flows and water chemistry in hydrobiogeochemical transport models can lead to new insights about POP behaviour in rivers. As most riverine POPs are associated with suspended sediments (SS) or dissolved organic carbon (DOC), coupled models simulating SS and DOC can provide additional insights about POPs behaviour. Coupled simulations of river flow, DOC, SS and POP dynamics offer the possibility of improved predictions of contaminant fate and fluxes by leveraging the additional information in routine water quality time series. Here, we present an application of a daily time step dynamic coupled multimedia fate and hydrobiogeochemical transport model (The Integrated Catchment (INCA) Contaminants model) to simulate the behaviour of selected PCB congeners in the River Thames (UK). This is a follow-up to an earlier study where a Level III fugacity model was used to simulate PCB behaviour in the Thames. While coupled models are more complex to apply, we show that they can lead to much better representation of POPs dynamics. The present study shows the importance of accurate sediment and organic carbon simulations to successfully predict riverine PCB transport. Furthermore, it demonstrates the important impact of short-term weather variation on PCB movement through the environment. Specifically, it shows the consequences of the severe flooding, which occurred in early 2014 on sediment PCB concentrations in the River Thames.

An INCA model for pathogens in rivers and catchments: Model structure, sensitivity analysis and application to the River Thames catchment, UK.

Pathogens are an ongoing issue for catchment water management and quantifying their transport, loss and potential impacts at key locations, such as water abstractions for public supply and bathing sites, is an important aspect of catchment and coastal management. The Integrated Catchment Model (INCA) has been adapted to model the sources and sinks of pathogens and to capture the dominant dynamics and processes controlling pathogens in catchments. The model simulates the stores of pathogens in soils, sediments, rivers and groundwaters and can account for diffuse inputs of pathogens from agriculture, urban areas or atmospheric deposition. The model also allows for point source discharges from intensive livestock units or from sewage treatment works or any industrial input to river systems. Model equations are presented and the new pathogens model has been applied to the River Thames in order to assess total coliform (TC) responses under current and projected future land use. A Monte Carlo sensitivity analysis indicates that the input coliform estimates from agricultural sources and decay rates are the crucial parameters controlling pathogen behaviour. Whilst there are a number of uncertainties associated with the model that should be accounted for, INCA-Pathogens potentially provides a useful tool to inform policy decisions and manage pathogen loading in river systems.

Effects of afforestation on runoff and sediment load in an upland Mediterranean catchment.

This paper assesses annual and seasonal trends in runoff and sediment load resulting from climate variability and afforestation in an upland Mediterranean basin, the Ribera Salada (NE Iberian Peninsula). We implemented a hydrological and sediment transport distributed model (TETIS) with a daily time-step, using continuous discharge and sediment transport data collected at a monitoring station during the period 2009-2013. Once calibrated and validated, the model was used to simulate the hydrosedimentary response of the basin for the period 1971-2014 using historical climate and land use data. Simulated series were further used to (i) detect sediment transport and hydrologic trends at different temporal scales (annual, seasonal); (ii) assess changes in the contribution of extreme events (i.e. low and high flows) and (ii) assess the relative effect of forest expansion and climate variability on trends observed by applying a scenario of constant land use. The non-parametric Mann-Kendall test indicated upward trends for temperature and decreasing trends (although non-significant) for precipitation. Downward trends occurred for annual runoff, and less significantly for sediment yield. Reductions in runoff were less intense when afforestation was not considered in the model, while trends in sediment yield were reversed. Results also indicated that an increase in the river's torrential behaviour may have occurred throughout the studied period, with low and high flow events gaining importance with respect to the annual contribution, although its magnitude was reduced over time.

Surface enhanced Raman scattering, electronic spectrum and Mulliken charge distribution in the normal modes of bis(diethyldithiocarbamate)zinc(II) complex.

Surface-enhanced Raman scattering (SERS) was used to study the interactions of the normal modes of the bis(diethyldithiocarbamate)zinc(II) complex, [Zn(DDTC)2], on nano-structured silver surfaces. The electronic spectrum of this complex was measured and the charge transfer bands were assigned through the TD-PBE1PBE procedure. To see the electronic dispersion, the Mulliken electronic charges were calculated for each normal mode and correlated with the SERS effect. Full assignment of the SERS spectra was also supported by carefully analysis of the distorted geometries generated by the normal modes.

DFT: B3LYP/6-311G (d, p) vibrational analysis of bis-(diethyldithiocarbamate)zinc(II) and natural bond orbitals.

Theoretical and experimental bands have been assigned for the Fourier Transform Infrared (FT-IR) and Fourier Transform Raman (FT-Raman) spectra of the bis-(diethydithiocarbamate)Zn(II) complex, [Zn(DDTC)(2)]. The calculations and spectra interpretation have been based on the DFT/B3LYP method, infrared and Raman second derivative spectra as well as band deconvolution analysis. To assign the metal-ligand normal modes the deviation percentage of the geometrical parameters was used. Results confirms a pseudo tetrahedral structure around the Zn(II) cation. The calculated infrared and Raman spectra has an excellent agreement with the experimental spectra. The Natural Bond Orbital analysis (NBO) was carried out as a way to study the Zn(II) hybridization leading to the pseudo tetrahedral geometry of the framework of the [Zn(DDTC)(2)] complex, and to study also which are the donor NBO and the acceptor NBO in meaningful charge transfer through the Second Order Perturbation Theory Analysis of Fox Matrix in NBO basis.

Nonkinetic modeling of the mechanical unfolding of multimodular proteins: theory and experiments.

We introduce and discuss a novel approach called back-calculation for analyzing force spectroscopy experiments on multimodular proteins. The relationship between the histograms of the unfolding forces for different peaks, corresponding to a different number of not-yet-unfolded protein modules, is exploited in such a manner that the sole distribution of the forces for one unfolding peak can be used to predict the unfolding forces for other peaks. The scheme is based on a bootstrap prediction method and does not rely on any specific kinetic model for multimodular unfolding. It is tested and validated in both theoretical/computational contexts (based on stochastic simulations) and atomic force microscopy experiments on (GB1)(8) multimodular protein constructs. The prediction accuracy is so high that the predicted average unfolding forces corresponding to each peak for the GB1 construct are within only 5 pN of the averaged directly-measured values. Experimental data are also used to illustrate how the limitations of standard kinetic models can be aptly circumvented by the proposed approach.