Summary of Advances in Heat-Pulse Methods: Measuring Near-Surface Soil Water Content

Surface layer soil water content is important for evaporation, surface energy balance, seed germination, residue decomposition, microbial activity, and many other biological, chemical, and physical processes. The standard method (i.e., the gravimetric method) for measuring soil water content requires destructive sampling and is unsuitable for continuous measurement. Techniques such as neutron thermalization and time domain reflectometry suffer relatively large errors in measuring soil water content near the surface. In a recent Methods of Soil Analysis article, the authors present the principles and procedures for using a heat-pulse sensor to determine near-surface soil water content

Determining In-situ Unsaturated Soil Hydraulic Conductivity at a Fine Depth Scale with Heat Pulse and Water Potential Sensors

Unsaturated hydraulic conductivity (K) of surface soil changes substantially with space and time, and it is of great importance for many ecological, agricultural, and hydrological applications. In general, K is measured in the laboratory, or more commonly, predicted using soil water retention curve and saturated hydraulic conductivity. In the field, K can be determined through infiltration experiments. However, none of these approaches are capable of continuously monitoring K insitu at fine depth scales. In this study, we propose and investigate an approach to continuously estimate fine depth-scale K dynamics under field conditions. Evaporation rate and change in water storage in a near-surface soil layer are measured with the heat pulse method. Then, water flux density at the lower boundary of the soil layer is estimated from evaporation rate, change in water storage, and rainfall or irrigation rate using a simple water balance approach. Finally, K values at different soil depths are derived using the Buckingham-Darcy equation from water flux densities and measured water potential gradients. A field experiment is performed to evaluate the performance of the proposed approach. K values at 2-, 4-, 7.5-, and 12.5-cm depths are estimated with the new approach. The results show that in-situ K estimates vary with time following changes in soil water content, and the K-water content relationship changes with depth due to the difference in bulk density. In-situ estimated K-matric potential curves agree well with those measured in the laboratory. In-situ K estimates also show good agreement with the Mualem-van Genuchten model predictions, with an average root mean square error in log10 (K, mm h-1) of 0.54 and an average bias of 0.17. The new approach provides reasonable in-situ K estimates and has potential to reveal the influences of natural soil conditions on hydraulic properties as they change with depth and time

Strategic implications of counter-geoengineering: clash or cooperation?

Solar geoengineering has received increasing attention as an option to temporarily stabilize global temperatures. A key concern is that heterogeneous preferences over the optimal amount of cooling combined with low deployment costs may allow the country with the strongest incentive for cooling, the so-called free-driver, to impose a substantial externality on the rest of the world. We analyze whether the threat of counter-geoengineering technologies capable of negating the climatic effects of solar geoengineering can overcome the free-driver problem and tilt the game in favour of international cooperation. Our game-theoretical model of countries with asymmetric preferences allows for a rigorous analysis of the strategic interaction surrounding solar geoengineering and counter-geoengineering. We find that counter-geoengineering prevents the free-driver outcome, but not always with benign effects. The presence of counter-geoengineering leads to either a climate clash where countries engage in a non-cooperative escalation of opposing climate interventions (negative welfare effect), a moratorium treaty where countries commit to abstain from either type of climate intervention (indeterminate welfare effect), or cooperative deployment of solar geoengineering (positive welfare effect). We show that the outcome depends crucially on the degree of asymmetry in temperature preferences between countries

Approaches for estimating unsaturated soil hydraulic conductivities at various bulk densities with the extended Mualem-van Genuchten model

The Mualem-van Genuchten model has been widely used for estimating unsaturated soil hydraulic conductivity (Ku) from measured saturated hydraulic conductivity (Ks) and fitted water retention curve (WRC) parameters. Soil bulk density (ρb) variations affect the accuracy of Ku estimates. In this study, we extend the Mualem-van Genuchten model to account for the ρb effect with ρb-related WRC and Ks models. We apply two functions (A and B) that relate the van Genuchten WRC model to ρb and two models (1 and 2) that estimate Ks with various ρb. By combining the ρb-related WRC functions and Ks models, we develop four integrated approaches (i.e., A1, A2, B1, and B2) for estimating Ku at various ρb. Kumeasurements made on five soils with various textures and ρb are used to evaluate the accuracy of the four approaches. The results show that all approaches produce reasonable Ku estimates, with average root mean square errors (RMSEs) less than 0.35 (expressed in dimensionless unit because logarithmic Ku values are used). Approach A2, with an average RMSE of 0.25, agrees better with Ku measurements than does Approach A1 that has an average RMSE of 0.28. This is because Model 2 accounts for the WRC shape effect near saturation. Approaches A1 and A2 give more accurate Ku estimates than do Approaches B1 and B2 which both have average RMSEs of 0.35, because Function A performs better in estimating WRCs than does Function B. The proposed approaches could be incorporated into simulation models for improved prediction of water, solute, and gas transport in soils

Bulk Density Effects on Soil Hydrologic and Thermal Characteristics: a Numerical Investigation

Soil bulk density (ρb) is commonly treated as static in studies of land surface dynamics. Magnitudes of errors associated with this assumption are largely unknown. Our objectives were to: i) quantify ρb effects on soil hydrologic and thermal properties, and ii) evaluate effects of ρb on surface energy balance and heat and water transfer. We evaluated six soil properties, volumetric heat capacity, thermal conductivity, soil thermal diffusivity, water retention characteristics, hydraulic conductivity, and vapor diffusivity, over a range of ρb, using a combination of six models. Thermal conductivity, water retention, hydraulic conductivity, and vapor diffusivity were most sensitive to ρb, each changing by fractions greater than the associated fractional changes in ρb. A 10% change in ρb led to 10-11% change in thermal conductivity, 6-11% change in saturated and residual water content, 49-54% change in saturated hydraulic conductivity, and 80% change in vapor diffusivity. Subsequently, three field seasons were simulated with a numerical model (HYDRUS-1D) for a range of ρb values. When ρb increased from 1.2 to 1.5 Mg m-3; 25% increase, soil temperature variation decreased by 2.1°C in shallow layers and increased by 1°C in subsurface layers. Surface water content differed by 0.02 m3 m-3 for various ρb values during drying events but differences mostly disappeared in the subsurface. Matric potential varied by \u3e100 m of water. Surface energy balance showed clear trends with ρb. Latent heat flux decreased 6%, sensible heat flux increased 9%, and magnitude of ground heat flux varied by 18% with a 25% ρb increase). Transient ρb impacted surface conditions and fluxes, and clearly it warrants consideration in field and modeling investigations

Quantum mechanical bespoke force fields for computer-aided drug design

PhD ThesisThe ability to accurately model complex biological processes such as protein-ligand binding with an atomistic level of detail is critical to their thorough understanding. Typically a molecular mechanics simulation is used, which represents the system using a force eld that is a physically motivated linear combination of empirically parameterised potentials. Traditionally their parameterisation has involved the recreation of experimental and quantum mechanical data for a target set of representative structures, ranging from small molecules to peptides. This potentially limits the progress of general transferable force elds to time and labour-intensive incremental improvements. In this thesis, we aim to challenge this \parameterise once and transfer" philosophy, with that of a transferable parametrisation methodology that can be readily applied to new systems with a consistent level of accuracy. We collect together recently developed force eld parameterisation techniques from the literature to develop a protocol suitable to derive virtually all required force eld parameters for small molecules directly from quantum mechanics. This protocol forms the basis of the QUantum mechanical BEspoke force eld (QUBE) and is delivered to users through a reliable and extensible software toolkit named QUBEKit. Here we extensively benchmark the methodology and software presented through typical force eld performance metrics which involve the prediction of thermodynamical properties of small organic molecules. In this regard, we achieve very competitive accuracy with popular general transferable force elds such as OPLS which have been extensively optimised to reproduce such properties. We also demonstrate how the QUBE force eld is a suitable alternative in a computer-aided drug design setting via the retrospective calculation of the relative binding free energies of 17 inhibitors of p38 MAP kinase. Again good agreement with both experiment and transferable force elds is achieved despite this being the rst generation of the force eld. The results of this work are then particularly important to those studying systems which are not covered or inaccurately represented by standard transferable force elds, as we present an accurate framework towards their complete parameterisation

Summary of Thermo–Time Domain Reflectometry Method: Advances in Monitoring In Situ Soil Bulk Density

Soil bulk density (ρb) is a key indicator of soil compaction and soil health that relates to water infiltration, plant rooting depth, nutrient availability, and soil microbial activity. Under field conditions, ρb usually varies with time and depth because of agronomic practices, root growth, and environmental processes (e.g., rainfall events, wetting/drying, and freezing/thawing). The traditional technique (i.e., the coring method) for determining ρb has the problems of destructive sampling, labor intensive, and is unable to capture the spatial and temporal variations. In a chapter of the recent Methods of Soil Analysis book, we present a review of the theory, instrumentation, and procedures of the thermo–time domain reflectometry (thermo-TDR) technique for monitoring in situ ρb (Lu et al., 2017)

Approaches for estimating soil water retention curves at various bulk densities with the extended van Genuchten model

Soil bulk density (ρb) variations influence soil hydraulic properties, such as the water retention curve (WRC), but they are usually ignored in soil water simulation models. We extend the van Genuchten WRC model parameters to account for ρb variations using a series of empirical expressions. WRC measurements made on eight soils with various ρb, and textures are used to calibrate these ρb‐related empirical equations. Accordingly, two approaches are developed to estimate WRCs of soils at various ρb. Another eight soils with a wide range of ρb and textures are used to evaluate the accuracy of the new approaches. Approach 1 estimates WRCs for each soil at various ρb using a WRC measurement made at a reference ρb and the soil texture fractions. This approach gives reasonable WRC estimates for the eight validation soils, with an average root‐mean‐square error (RMSE) of 0.025 m3/m3 and an average determination coefficient (R2) of 0.94. For Approach 2, a WRC measurement made at a reference ρb and one additional water content‐matric potential value measured at a different ρb value are used, which produces WRC estimates with an average RMSE of 0.017 m3/m3 and an average R2 of 0.97. The methodology used in Approach 2 is also applied to the Brooks and Corey WRC model to obtain accurate and precise WRC estimates. The proposed approaches have the potential to be incorporated into simulation models for estimating soil hydraulic properties that are affected by transient and variable ρb

Field Test and Sensitivity Analysis of a Sensible Heat Balance Method to Determine Soil Ice Contents

Feasibility of the sensible heat balance (SHB) method for determining in situ soil ice content with heat pulse (HP) sensors was evaluated using field measurements. The required accuracy of HP sensor measurements for SHB was further assessed with a sensitivity analysis. Improving accuracy of thermal conductivity measurements and using short time steps are necessary to accurately estimate ice contents with the SHB method. Soil ice content impacts winter vadose zone hydrology. It may be possible to estimate changes in soil ice content with a sensible heat balance (SHB) method, using measurements from heat pulse (HP) sensors. Feasibility of the SHB method is unknown because of difficulties in measuring soil thermal properties in partially frozen soils. The objectives of this study were (i) to examine the SHB method for determining in situ ice content, and (ii) to evaluate the required accuracy of HP sensors for use in the SHB method. Heat pulse sensors were installed in a bare field to measure soil temperatures and thermal properties during freezing and thawing events. In situ soil ice contents were determined at 60-min intervals with SHB theory. Sensitivity of the SHB method to temperature, heat capacity, thermal conductivity, and time step size was analyzed based on numerically produced soil freezing and thawing events. The in situ ice contents determined with the SHB method were sometimes unrealistically large or even negative. Thermal conductivity accuracy and time step size were the key factors contributing to SHB errors, while temperature and heat capacity accuracy had less influence. Ice content estimated with a 15-min SHB time step was more accurate than that estimated with a 60-min time step. Sensitivity analysis indicated that measurement errors in soil temperature and thermal conductivity should be less than ±0.05°C and ±20%, respectively, but the error in the soil heat capacity could vary by ±50%. Thus, improving the accuracy of thermal conductivity measurements and using short time steps are required to accurately estimate soil ice contents with the SHB method

Using saturation mutagenesis to explore substrate specificity and catalysis in benzoylformate decarboxylase

poster abstractBenzoylformate decarboxylase (BFDC) from Pseudomonas putida and pyruvate decarboxylase (PDC) from Zymomonas mobilis are thiamin diphosphate (ThDP)-dependent enzymes. The two share a common three-dimensional structure and catalyze a similar chemical reaction, i.e., decarboxylation of 2-keto acids. However, they vary significantly in their substrate utilization pattern. In particular, BFDC has extremely limited activity with pyruvate, while PDC has no activity with benzoylformate. Both enzymes also catalyze stereospecific carboligation reactions that are of commercial interest, again with a different range of substrates. In order to identify similarities and differences on a molecular level, and to reveal factors responsible for substrate specificity and enantioselectivity, the X-ray structures BFDC and PDC were compared. Residues identified in this process were subjected to site-directed mutagenesis. The results show that, although it was not possible to simply interchange substrates, it was possible to engineer enzymes that had distinctly different substrate specificities while retaining excellent kinetic activity. However, it also became apparent that a more general approach was needed. Towards this end we developed a screening procedure for BFDC to enable us to use saturation mutagenesis to examine residues involved in substrate specificity. During the development of the methodology it became clear that it was possible to use this approach to explore residues involved in catalysis by BFDC. Here we describe the unexpected results obtained using saturation mutagenesis on putative catalytic residues. In addition we report towards converting BFDC into an efficient pyruvate decarboxylase