RNA secondary structure design

We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called designable. We implemented a branch-and-bound algorithm that is able to do an exhaustive search within the sequence space, i.e., gives an exact answer whether such a sequence exists. The bound required by the branch-and-bound algorithm are calculated by a dynamic programming algorithm. We consider different alphabet sizes and an ensemble of random structures, which we want to design. We find that for two letters almost none of these structures are designable. The designability improves for the three-letter case, but still a significant fraction of structures is undesignable. This changes when we look at the natural four-letter case with two pairs of complementary bases: undesignable structures are the exception, although they still exist. Finally, we also study the relation between designability and the algorithmic complexity of the branch-and-bound algorithm. Within the ensemble of structures, a high average degree of undesignability is correlated to a long time to prove that a given structure is (un-)designable. In the four-letter case, where the designability is high everywhere, the algorithmic complexity is highest in the region of naturally occurring RNA.Comment: 11 pages, 10 figure

A hydrochemical assessment of groundwater-surface water interaction in the Woodham Burn, a Magnesian Limestone catchment in County Durham

The interaction between groundwater and surface water, in particular in the hyporheic zone, is recognised to influence chemical fluxes between river and groundwater and to transform reactive chemistries such as nutrients or legacy contaminants. Characterising this connectivity in the Skerne catchment in Co. Durham has been recognised to be important by the Environment Agency (EA) in order to protect the underlying Magnesian Limestone aquifer and dependent features. Of particular concern is the presence of an eastward moving, sulphate-rich, mine water plume related to the recovery of groundwater levels in the underlying Coal Measures strata and mine workings. Building on a previous investigation across the entire Skerne catchment, this work, in collaboration with the EA, aimed to understand the existence of hydraulic connection between groundwater and surface water and the hyporheic zone characteristics in a 500 m stretch of the Woodham Burn, a tributary of the Skerne. We have employed multiple methods, both at the reachscale and smaller sediment-scale, for identifying source areas of sulphate to the stream, characterising the subsurface flow and estimating the controls on sulphate fluxes and potential natural attenuation. The Woodham Burn was monitored during three sampling events in: April 2018, August 2018, and February 2019. The stream water chemistry survey has confirmed sulphate concentrations in excess of the drinking water standard of 250 mg/l, with a median of 510 mg/l in the surface water, range 235- 790 mg/l. Stream flow measurements complementary to the water chemistry analysis were not possible and therefore loads (flow multiplied by concentration) of sulphate could not be calculated. Given the lack of tributaries, the changes in surface water chemistry were, nevertheless, useful to attribute the observed changes to groundwater losses or gains, where groundwater and surface water concentrations are significantly different. The spatial survey of downstream changes in stream water chemistry has delineated a sulphate-rich recharge zone within the study reach, which is very localised, with sulphate concentrations up to 800 mg/l and electrical conductivity of 2000 µS/cm. The source appears to be groundwater discharging directly into the stream channel and in the form of a seep on the western bank. The contribution of this source to the stream was quantified as up to 50 percent increase in dissolved sulphate in surface water. An additional area potentially recharging sulphate to the stream, more diffuse in nature, was identified through analysis of the water-soluble fraction of soil samples collected by augers and additional bank seepage measurements and it corresponds to the northern banks upstream of the first monitoring point. Temperature vertical profiling of the riverbed along the 500 m study reach together with a corresponding survey of specific electrical conductivity (SEC) variation in the surface water were used to further detect areas of potential flow of surface water to groundwater or flow of groundwater to surface water, and to inform the site selection for the monitoring of subsurface flow at smaller scale with piezometers and minipiezometers. At four locations, piezometers were installed with data loggers to provide continuous observations of hydraulic heads, temperature, and (at two points) SEC: two paired piezometers of shallow (0.4 m) and deeper (1.4 m) depth at three of the locations and only a single shallow piezometer for one site. Due to the loss of the surface water logger after a storm event, precise water level fluctuations in Woodham Burn were unknown, and recorded fluctuations in the subsurface were more difficult to correlate. At the same locations, plus an additional one, a network of multilevel minipiezometers (two to three per site) were driven into the hyporheic zone to a fixed depth of 0.9 m below the riverbed and used to draw pore water from 10, 20, 50 and 90 cm depth. The evidence from vertical gradients of conservative elements, chloride and lithium, measured in each multilevel minipiezometer, and evidence from the diurnal temperature variations and hydraulic head from logged data, converged to indicate an increase of hyporheic exchange flow (HEF) moving downstream in the burn, corresponding to the transition in the superficial deposits from alluvium to lacustrine deposits, while the most upstream sites showed the near absence of HEF and at least one clearly gaining reach in correspondence of the sulphate-rich instream discharge. ix Evaluation of natural attenuation in the hyporheic zone was carried out via comparison of conservative and non-conservative solute gradients. In most of the sites where there was sufficient HEF, both nitrate and sulphate showed various extents of non-conservative behaviour compared to chloride in the subsurface flow. In particular, the most significant losses of nitrate were observed in piezometers at the most downstream section of the reach (-48% to -98%). Sulphate losses were generally lower than those for nitrate and varied greatly (9% to 100%), often larger at depth. Although nitrate and sulphate losses were observed during surface water downwelling in the studied hyporheic zone, a correspondent decrease in stream water concentrations was not evident. It is recommended to test the significance of hyporheic natural attenuation to improve the stream water quality at catchment scale, by carrying out surface water flow measurements combined with water quality analysis, which enable calculation of mass gains and losses to identify the net flux integrated over the entire stream. The analysis of the deep hyporheic zone chemistry, the least affected by shallow hyporheic exchange of downwelling surface water, gave insights into hydrochemical differences along the reach and indicates potentially distinct groundwater sources. These differences appear to be related to geology: the most upstream monitoring locations sited on the alluvium have greater similarities to the Magnesian Limestone aquifer, as inferred by cluster analysis with additional EA groundwater monitoring boreholes. As previously identified points of limited HEF and groundwater dominated hyporheic water, these locations plausibly represent a groundwater recharge zone. On the other hand, the most downstream points located on the lacustrine deposits show a different hyporheic zone composition, distinctly closer to hyporheic waters previously sampled from Rushyford Beck, also on lacustrine deposits. Beside these hydrochemical differences, a greater one is represented by the discrete spring (Bubbly Spring) discharging through the stream bed and western stream banks. Its chemistry has strong similarities to other seeps in the burn and also to Stony Hall C borehole water, which is sourced from the Coal Measures. The spring composition (Mg-SO4 water type) was very stable throughout the monitoring period and distinctively enriched in SO4 (median 811 mg/l) together with Sr (median 984 μg/l) , Li (median 162 μg/l), Rb (median 7.19 μg/l) and U (median 4.04 μg/l) compared to all the other waters in Woodham Burn, while it was lower in Si, Ba, Mn and Fe. Two, both plausible, reaction paths can explain the spring composition: one is gypsum dissolution and dedolomitisation, the other one is acid neutralisation of coal mine water through the dissolution of dolomite. To explain the physical processes underpinning the emergence of this groundwater enriched in sulphate and the origin of this sulphate further investigation is needed. In particular residence time studies and isotope analysis of water and dissolved sulphate are recommended. To gain a broader perspective on groundwater discharge areas a spatial hydrochemical survey of springs and seeps in the catchment should also be undertaken

Investigation of sulphate sulphur isotope variations in the Skerne Magnesian Limestone water body

This report presents the results of a sulphur isotope investigation undertaken in the Skerne catchment, located in County Durham, north of Darlington, to investigate the source of groundwater sulphate in the Magnesian Limestone Aquifer. Groundwater and surface waters in the catchment are at risk from a number of current and historic anthropogenic activities. Sulphate is the biggest risk to the public water supplies; as there is currently no cost-effective treatment available and it could render supplies unusable. The elevated sulphate could be both naturally occurring, due to the presence of gypsum or anhydrite bands in the Magnesian Limestone, or it could be due to abandoned coal mine water, or even saline intrusion pollution. Because of the large difference in the sulphate sulphur isotope composition expected between “marine sulphate”, including sulphate derived from marine evaporites, and “non-marine sulphate” derived from the oxidation of sulphide in the coal seams and mine workings, sulphur isotopes were considered promising tracers to discern mine water sources from natural Permian evaporite sources of sulphate. A survey was carried out at 28 sites where groundwater was sampled in July 2018 from boreholes in the Magnesian Limestone Aquifer and in the Coal Measures, following a pilot study comprising 7 boreholes in July 2017. A small number of surface waters, hyporheic zone waters, springs, and soil leachates, sampled during 2017-2018, were also analysed for sulphur isotopes to complement the borehole data. This has allowed the characterisation of the sulphur isotope composition of potential sources of dissolved sulphate. Most of the Magnesian Limestone aquifer groundwaters cluster close to the Global Meteoric Water Line (GMWL) on the dual water δ 18O and δ2H graph with no evidence of mixing with Narich coal mine water, the latter being more depleted in 18O and 2H; there is a small number of boreholes immediately in proximity of the coal seam boreholes, clearly showing signs of water mixing. With higher δ18O and δ2H than the main Magnesian Limestone group, and slightly offset from the GMWL, is also a small group of Magnesian Limestone boreholes. Repeated sampling would better discern the different recharge paths suggested by this single sampling event in July 2018. Groundwaters associated with the worked and unworked coal seam boreholes in this study are of two water types: sodium sulphate (Na–SO4) and sodium bicarbonate (Na–HCO3) waters, variably enriched in dissolved sulphate. Two δ 34S measurements of the dissolved sulphate in the Na–SO4 coal seam boreholes are +13.1‰ and +23.4‰. The lack of the more typical 34S-depleted sulphate derived from the oxidation of pyrite is hence apparent. A similar range of high sulphate δ 34S values has been described in recent studies, and attributed to deep coal mine systems. From a review of published δ34S values for marine evaporites, groundwaters containing sulphate solely derived from the dissolution of Permian marine evaporites are characterised by 34Senriched sulphate (δ34S values range from +8.2 to +11.1‰). There is, therefore, less of a contrasting isotope signature between potential “evaporite” and “coal mine water” end-members. For example, one sample of coal mine water with δ 34S values of +13.1‰ is not too dissimilar to the average Permian evaporite sulphate with δ 34S value of around +10‰. This makes discrimination of the dissolved sulphate sources based on sulphur isotope less certain, especially at low sulphate concentrations. To help the data interpretation, we have modelled the sulphate and sulphur isotope compositions of mixtures of hypothetical end-members and used the evidence from these simulations to constrain possible groundwater contributions and mixing. In particular we simulate how the HARDWICK HALL borehole, representing the Magnesian Limestone aquifer background, with a sulphate concentration of 89 mg/l, and a δ34S value of +1.0‰, evolves during mixing with the following end-members: i) the coal mine waters in this study, ii) a Permian evaporite source, iii) seawater and iv) acid mine drainage. A summary of the data interpretation based on the above modelling is as follows. Over the mine plume area, inputs of coal mine water-derived sulphate are significant in at least one Magnesian Limestone borehole, and detectable in others, supported by the water isotope δ 18O and δ2H data, indicating for these samples water mixing between the coal mine water and the Magnesian Limestone aquifer. Among the Magnesian Limestone boreholes, where gypsum or anhydrite were noted in the borehole logs, only DALTON PIERCY NO 3 and NO 6 boreholes have high sulphate concentrations and display constant δ 34S values of +10.2‰. Given how close this value is to the Permian evaporites’ δ34S values, it could be plausibly explained by a gypsum dissolution source, although a “coal mine water” contribution with a δ34S signature of +13‰ cannot be totally excluded, as shown by the mixing curves. Many of the Magnesian Limestone boreholes with a sulphate concentration around 100 mg/l (range 85–130 mg/l) are characterised instead by a low δ 34S range (-0.7 to +7.2‰). For most of these low sulphate Magnesian Limestone boreholes, uncertainties in discriminating the source of sulphate are higher. The contribution of sulphate from seawater is difficult to discern in the present data for the saline waters of HART RESERVOIR and HARTLEPOOL IND ESTATE REPLACEMENT boreholes, with similar δ34S values of +21.1‰ and +27‰, as they fall far away from the Seawater–Magnesian Limestone mixing line. Many samples fall far outside of these mixing envelopes, suggesting non-conservative behaviour of the sulphate. The very high δ34S and low sulphate concentrations can be interpreted as a possible sign of reduction of sulphates and enrichment in the heavier 34S isotope of the residual (low concentration) sulphate. Additional samples obtained during this study include: i) A spring in the Ford Formation from AYCLIFFE QUARRY to the south east of Aycliffe Village which provides an additional background sample characterised for sulphur isotopes. The water has a SO4 of 69 mg/l and a δ34S value of +2.3‰ and well resembles the composition of HARDWICK HALL borehole. ii) A Mg–SO4 spring, sampled in Woodham Burn and described in previous studies for its impact on the surface water quality because of its high sulphate concentrations of ~800 mg/l. It has a stable δ34S value of ~ +5.5‰. iii) a surface water impacted by mine water inflow with a Mg–SO4 composition, and a δ34S value of +6.9‰. The δ34S value of +5.5‰ of the Mg-SO4 spring at Woodham Burn points to a contribution of low δ 34S-sulphate, as expected from the oxidation of pyrite. These data support the mechanism, hypothesised in Palumbo-Roe et al. (2020) to account for the spring composition, of dissolution of dolomite in the presence of acidic water, where the source of acidity comes from coal mine water due to the oxidation of pyrite. There is a much narrower and lower range of δ 34S in surface water compared to the groundwater samples. With most δ 34S values less than +7‰, none of the high values measured in the boreholes were noted in the surface water, hyporheic zone or soil leachate samples, except for two samples in the hyporheic zone of Woodham Burn with δ 34S +36.3‰ and +13.4‰, values taken as further evidence of the sulphate reduction during the 2018 summer indicated by the hydrochemistry. Recommendations for future work, building upon these findings, are suggested

Temporal interpolation of groundwater level hydrographs for regional drought analysis using mixed models

Large-scale studies of the spatial and temporal variation of groundwater drought status require complete inventories of groundwater levels on regular time steps from many sites so that a standardised drought index can be calculated for each site. However, groundwater levels are often measured sporadically, and inventories include missing or erroneous data. A flexible and efficient modelling framework is developed to fill gaps and regularise data in such inventories. It uses linear mixed models to account for seasonal variation, long-term trends and responses to precipitation and temperature over different temporal scales. The only data required to estimate the models are the groundwater level measurements and freely available gridded weather products. The contribution of each of the four types of trends at a site can be determined and thus the causes of temporal variation of groundwater levels can be interpreted. Validation reveals that the models explain a substantial proportion of groundwater level variation and that the uncertainty of the predictions is accurately quantified. The computation for each site takes less than 130 s and requires little supervision. Hence, the approach is suitable to be upscaled to represent the variation of groundwater levels in large datasets consisting of thousands of boreholes

A conceptual model of the groundwater contribution to streamflow during drought in the Afon Fathew catchment, Wales

In 2022 BGS was commissioned by Dŵr Cymru Welsh Water (DCWW) to undertake desk and field investigations to develop a conceptual understanding of the contribution of groundwater to streamflow during drought in the Afon Fathew, Wales. This report details the findings of these investigations. In addition to a desk study, two field visits were completed to survey water features in the catchment, take samples for groundwater residence time indicators, and undertake a passive seismic (Tromino) geophysical survey. The results of the desk study and field visits were combined with flow accretion profile data to develop a conceptual model of groundwater flow to the Afon Fathew during drought, described herein. The Fathew is underlain by a bedrock of silty mudstones which are traditionally considered to be poor aquifers. In the Fathew catchment there is evidence from boreholes for local-scale groundwater flow in the bedrock within fractures and other discontinuities. An upper weathered layer, in combination with faulting and folding patterns, is likely to control the geometry and magnitude of bedrock groundwater flow systems and the location of springs. The residence time indicator data suggest that groundwater in the bedrock is over 40 years old. Estimated discharge from bedrock springs (< 2 l/s, 0.17 Ml/day) is very small relative to the total flow in the Fathew and tributary inflows. The Tromino has shown the superficial deposits in the catchment to be highly heterogeneous in the valley bottom. Changes in the likely permeability and areal extent of the superficial deposits going down the valley bottom correspond to changes in river flows in the Fathew based on the accretion profiles. The Fathew and its tributaries are losing over well drained alluvial gravels, and gaining over low permeability lacustrine and clay-ey alluvial deposits. The Fathew is likely to be hydraulically isolated from the Dysynni catchment. 60% of low flow inflows to the Fathew are coming directly from upland tributary inflows. where very limited superficial deposits are present. In these upland settings during dry periods it is likely that the majority of discharge is coming from baseflow from bedrock. Baseflow support to the Fathew during drought periods can be conceptualised as a two-phase system: (1) Discharge from the superficial deposits to the river, particularly associated with the down-catchment variability in the permeability and thickness of the deposits, (2) Discharge from the weathered bedrock aquifer into the river, from both springs and tributary inflows. The contribution of these two processes is likely to vary as drought conditions develop. Moreover, flows in springs and tributaries may contribute to downstream storage within the superficial deposits, which may complicate the deconvolution of the Fathew river flow hydrograph into different flow components. This temporal sequencing requires further investigation. Further work such as groundwater and surface water monitoring during dry periods and electrical resistivity tomography may be beneficial to constrain these uncertainties

A fabrication guide for planar silicon quantum dot heterostructures

We describe important considerations to create top-down fabricated planar quantum dots in silicon, often not discussed in detail in literature. The subtle interplay between intrinsic material properties, interfaces and fabrication processes plays a crucial role in the formation of electrostatically defined quantum dots. Processes such as oxidation, physical vapor deposition and atomic-layer deposition must be tailored in order to prevent unwanted side effects such as defects, disorder and dewetting. In two directly related manuscripts written in parallel we use techniques described in this work to create depletion-mode quantum dots in intrinsic silicon, and low-disorder silicon quantum dots defined with palladium gates. While we discuss three different planar gate structures, the general principles also apply to 0D and 1D systems, such as self-assembled islands and nanowires.Comment: Accepted for publication in Nanotechnology. 31 pages, 12 figure

Groundwater quality: global challenges, emerging threats and novel approaches

Improving our understanding of groundwater quality threats to human health and the environment is essential to protect and manage groundwater resources effectively. This essay highlights some global groundwater quality challenges, describes key contaminant groups and threats of emerging concern, including antimicrobial resistance, and discusses novel approaches to assessing groundwater quality. Groundwater quality monitoring needs to improve significantly in order to effectively identify and mitigate threats to groundwater from historical, current and future pollution

Fluctuation-Facilitated Charge Migration along DNA

We propose a model Hamiltonian for charge transfer along the DNA double helix with temperature driven fluctuations in the base pair positions acting as the rate limiting factor for charge transfer between neighboring base pairs. We compare the predictions of the model with the recent work of J.K. Barton and A.H. Zewail (Proc.Natl.Acad.Sci.USA, {\bf 96}, 6014 (1999)) on the unusual two-stage charge transfer of DNA.Comment: 4 pages, 2 figure

Managing groundwater supplies subject to drought: perspectives on current status and future priorities from England (UK)

Effective management of groundwater resources during drought is essential. How is groundwater currently managed during droughts, and in the face of environmental change, what should be the future priorities? Four themes are explored, from the perspective of groundwater management in England (UK): (1) integration of drought definitions; (2) enhanced fundamental monitoring; (3) integrated modelling of groundwater in the water cycle; and (4) better information sharing. Whilst these themes are considered in the context of England, globally, they are relevant wherever groundwater is affected by drought