Discretely conservative meshfree principles for conservation laws.
Abstract not provided.
Trask, Nathaniel Albert↗
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Discretely conservative meshfree schemes for conservation laws.
Abstract not provided.
Trask, Nathaniel Albert↗
Sequence conservation of protein binding segments in intrinsically disordered regions
Highlights: • Sequence conservation in protein-binding segments in IDRs is analyzed. • Functionally constraint residues in protein-binding segments in IDRs are conserved. • Evolutionary distance should be considered in the comparison of IDRs. • Cryptic binding regions may influence sequence conservation of IDRs. Intrinsically disordered proteins are proteins with intrinsically disordered regions (IDRs) that do not adopt a globular structure in their free state. IDRs have unique regions having protein-binding segments of which play pivotal roles in many biological processes. The binding sites in IDRs are heterogeneous in terms of their sequence conservation: some are conserved and others are not. We have been running a database of intrinsically disordered proteins, IDEAL, and collecting such binding segments, which are called protean segments (ProSs), within it. In this study, we compared the sequence conservation of ProSs, structural domains (SDs), and IDRs other than ProSs (non-ProSs) and found that i) functionally constrained residues in ProSs tend to be conserved, ii) the distribution of conservation scores of ProSs is similar to those of SDs but not non-ProSs, and iii) ProSs found in human proteins are mostly conserved only in vertebrates. These results indicate that the conservation patterns in ProSs principally follow the general rules found in SDs. However, we need to consider evolutionary distance when comparing IDR sequences because ProSs can readily emerge and disappear over the course of protein evolution. Moreover, many ProSs may remain to be identified, which may account for the heterogeneity of the sequence conservation of IDRs.
60 APPLIED LIFE SCIENCES↗
Local conservation of energy in fully implicit PIC algorithms
We consider the issue of strict, fully discrete local energy conservation for a whole class of fully implicit local-charge- and global-energy-conserving particle-in-cell (PIC) algorithms. Earlier studies demonstrated these algorithms feature strict global energy conservation. However, whether a local energy conservation theorem exists (in which the local energy update is governed by a flux balance equation at every mesh cell) for these schemes is unclear. In this study, we show that a local energy conservation theorem indeed exists. We begin our analysis with the 1D electrostatic PIC model without orbit-averaging, and then generalize our conclusions to account for orbit averaging, multiple dimensions, and electromagnetic models (Darwin). In all cases, a temporally, spatially, and particle-discrete local energy conservation theorem is shown to exist, proving that these formulations (as originally proposed in the literature), in addition to being locally charge conserving and globally energy conserving, are strictly locally energy conserving as well. In contrast to earlier proofs of local conservation in the literature, which only considered continuum time, our result is valid for the fully implicit time-discrete version of all models considered, including important features such as orbit averaging. We demonstrate the local-energy-conservation property numerically with a paradigmatic numerical example.
97 MATHEMATICS AND COMPUTING↗
Stakeholder Support for Wildlife Conservation Funding Policies
State wildlife management agencies in the United States have depended on a “user-pay” funding model for conservation efforts that relies on revenue from hunting license sales and a federal excise tax on firearms, ammunition, and archery equipment. Declines in hunting participation, however, jeopardize sustainability of the current funding model. Ensuring support among stakeholders for wildlife management and conservation may require expanding sources of funding and incorporating the perspectives and values of a diversifying constituency into decision making processes. We used a web-based survey of wildlife-associated recreationists in Michigan, USA to evaluate support for a range of conservation funding policies. Respondents self-identified primarily as hunters (n = 2,558) or wildlife watchers (n = 942). We used binary logistic regression to evaluate support for four conservation funding policy options: state sales tax, lottery proceeds, extractive industry revenue, and a user-based tax on outdoor gear (i.e., “backpack tax”). Determinants of support varied by type of policy and stakeholder characteristics. We found no statistically significant differences between hunters and wildlife watchers in their support for conservation funding policies when accounting for other variables such as wildlife value orientations, engagement in stewardship behaviors, age, and gender. The industry-based policy achieved the greatest level of approval, while the backpack tax had the lowest. Respondents were mixed in their support of the sales tax and lottery proceeds options. Cluster analysis revealed three homogenous groups related to conservation funding policies: “strong support,” “mixed/opposed,” and “anti-backpack tax.” Clusters differed in their support for conservation funding policies and on psychological and demographic variables. The “strong support” and “anti-backpack tax” groups differed in their levels of stewardship engagement, knowledge of conservation funding mechanisms, and support for the backpack tax option. The “mixed-opposed” group tended to be older, less educated, and less likely to be a member of a conservation organization. Results suggest support for conservation funding differs by policy type and social and psychological characteristics of stakeholders. Based on differences in policy support revealed in this study, we suggest a multi-tiered approach to funding conservation and building on support among wildlife stakeholders to mitigate the looming funding crisis for state wildlife agencies.
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
Conservation of Transcription Start Sites within Genes across a Bacterial Genus
Transcription start sites (TSSs) lying inside annotated genes, on the same or opposite strand, have been observed in diverse bacteria, but the function of these unexpected transcripts is unclear. Here, we use the metal-reducing bacterium Shewanella oneidensis MR-1 and its relatives to study the evolutionary conservation of unexpected TSSs. Using high-resolution tiling microarrays and 5'-end RNA sequencing, we identified 2,531 TSSs in S. oneidensis MR-1, of which 18% were located inside coding sequences (CDSs). Comparative transcriptome analysis with seven additional Shewanella species revealed that the majority (76%) of the TSSs within the upstream regions of annotated genes (gTSSs) were conserved. Thirty percent of the TSSs that were inside genes and on the sense strand (iTSSs) were also conserved. Sequence analysis around these iTSSs showed conserved promoter motifs, suggesting that many iTSS are under purifying selection. Furthermore, conserved iTSSs are enriched for regulatory motifs, suggesting that they are regulated, and they tend to eliminate polar effects, which confirms that they are functional. In contrast, the transcription of antisense TSSs located inside CDSs (aTSSs) was significantly less likely to be conserved (22%). However, aTSSs whose transcription was conserved often have conserved promoter motifs and drive the expression of nearby genes. Overall, our findings demonstrate that some internal TSSs are conserved and drive protein expression despite their unusual locations, but the majority are not conserved and may reflect noisy initiation of transcription rather than a biological function.
bacterial genus↗
Impact of numerical choices on water conservation in the E3SM Atmosphere Model version 1 (EAMv1)
Abstract. The conservation of total water is an important numerical feature for global Earth system models. Even small conservation problems in the water budget can lead to systematic errors in century-long simulations. This study quantifies and reduces various sources of water conservation error in the atmosphere component of the Energy Exascale Earth System Model. Several sources of water conservation error have been identified during the development of the version 1 (V1) model. The largest errors result from the numerical coupling between the resolved dynamics and the parameterized sub-grid physics. A hybrid coupling using different methods for fluid dynamics and tracer transport provides a reduction of water conservation error by a factor of 50 at 1∘ horizontal resolution as well as consistent improvements at other resolutions. The second largest error source is the use of an overly simplified relationship between the surface moisture flux and latent heat flux at the interface between the host model and the turbulence parameterization. This error can be prevented by applying the same (correct) relationship throughout the entire model. Two additional types of conservation error that result from correcting the surface moisture flux and clipping negative water concentrations can be avoided by using mass-conserving fixers. With all four error sources addressed, the water conservation error in the V1 model becomes negligible and insensitive to the horizontal resolution. The associated changes in the long-term statistics of the main atmospheric features are small. A sensitivity analysis is carried out to show that the magnitudes of the conservation errors in early V1 versions decrease strongly with temporal resolution but increase with horizontal resolution. The increased vertical resolution in V1 results in a very thin model layer at the Earth's surface, which amplifies the conservation error associated with the surface moisture flux correction. We note that for some of the identified error sources, the proposed fixers are remedies rather than solutions to the problems at their roots. Future improvements in time integration would be beneficial for V1.
54 ENVIRONMENTAL SCIENCES↗
Impact of numerical choices on water conservation in the E3SM Atmosphere Model Version 1 (EAM V1)
The conservation of total water is an important numerical feature for global Earth system models. Even small conservation problems in the water budget can lead to systematic errors in century-long simulations for sea level rise projection. This study quantifies and reduces various sources of water conservation error in the atmosphere component of the Energy Exascale Earth System Model. Several sources of water conservation error have been identified during the development of the version 1 (V1) model. The largest errors result from the numerical coupling between the resolved dynamics and the parameterized sub-grid physics. A hybrid coupling using different methods for fluid dynamics and tracer transport provides a reduction of water conservation error by a factor of 50 at 1° horizontal resolution as well as consistent improvements at other resolutions. The second largest error source is the use of an overly simplified relationship between the surface moisture flux and latent heat flux at the interface between the host model and the turbulence parameterization. This error can be prevented by applying the same (correct) relationship throughout the entire model. Two additional types of conservation error that result from correcting the surface moisture flux and clipping negative water concentrations can be avoided by using mass-conserving fixers. With all four error sources addressed, the water conservation error in the V1 model is negligible and insensitive to the horizontal resolution. The associated changes in the long-term statistics of the main atmospheric features are small. A sensitivity analysis is carried out to show that the magnitudes of the conservation errors decrease strongly with temporal resolution but increase with horizontal resolution. The increased vertical resolution in the new model results in a very thin model layer at the Earth’s surface, which amplifies the conservation error associated with the surface moisture flux correction. We note that for some of the identified error sources, the proposed fixers are remedies rather than solutions to the problems at their roots. Future improvements in time integration would be beneficial for this model.
Zhang, Kai↗
A consistent and conservative volume distribution algorithm and its applications to multiphase flows using Phase-Field models
In the present study, the multiphase volume distribution problem, where there can be an arbitrary number of phases, is addressed using a consistent and conservative volume distribution algorithm. The proposed algorithm satisfies the summation constraint, the conservation constraint, and the consistency of reduction. The first application of the volume distribution algorithm is to determine the Lagrange multipliers in multiphase Phase-Field models that enforce the mass conservation, and a multiphase conservative Allen-Cahn model that satisfies the consistency of reduction is developed. A corresponding consistent and conservative numerical scheme is developed for the model. The multiphase conservative Allen-Cahn model has a better ability than the multiphase Cahn-Hilliard model to preserve under-resolved structures. The second application is to develop a numerical procedure, called the boundedness mapping, to map the order parameters, obtained numerically from a multiphase model, into their physical interval, and at the same time to preserve the physical properties of the order parameters. Along with the consistent and conservative schemes for the multiphase Phase-Field models, the numerical solutions of the order parameters are reduction consistent, conservative, and bounded, which are theoretically analyzed and numerically validated. Then, the multiphase Phase-Field models are coupled with the momentum equation by satisfying the consistency of mass conservation and the consistency of mass and momentum transport, thanks to the consistent formulation. Finally, it is demonstrated that the proposed model and scheme converge to the sharp-interface solution and are capable of capturing the complicated multiphase dynamics even when there is a large density and/or viscosity ratio.
42 ENGINEERING↗
A Local Macroscopic Conservative (LoMaC) Low Rank Tensor Method for the Vlasov Dynamics
Abstract In this paper, we propose a novel Local Macroscopic Conservative (LoMaC) low rank tensor method for simulating the Vlasov-Poisson (VP) system. The LoMaC property refers to the exact local conservation of macroscopic mass, momentum and energy at the discrete level. This is a follow-up work of our previous development of a conservative low rank tensor approach for Vlasov dynamics ( arXiv:2201.10397 ). In that work, we applied a low rank tensor method with a conservative singular value decomposition to the high dimensional VP system to mitigate the curse of dimensionality, while maintaining the local conservation of mass and momentum. However, energy conservation is not guaranteed, which is a critical property to avoid unphysical plasma self-heating or cooling. The new ingredient in the LoMaC low rank tensor algorithm is that we simultaneously evolve the macroscopic conservation laws of mass, momentum and energy using a flux-difference form with kinetic flux vector splitting; then the LoMaC property is realized by projecting the low rank kinetic solution onto a subspace that shares the same macroscopic observables by a conservative orthogonal projection. The algorithm is extended to the high dimensional problems by hierarchical Tuck decomposition of solution tensors and a corresponding conservative projection algorithm. Extensive numerical tests on the VP system are showcased for the algorithm’s efficacy.
Guo, Wei↗
The impact of a shade coffee certification program on forest conservation using remote sensing and household data
In recent years, shade coffee certification programs have attracted increasing attention from forest conservation and development organizations. The certification programs could be expected to promote forest conservation by providing a premium price to shade coffee producers. However, little is known about the significance of the conservation efforts generated by certification programs. In particular, the relationship between the impact of the certification and producer characteristics has yet to be examined. The purpose of this study, which was conducted in Ethiopia, was to examine the impact of a shade coffee certification program on forest conservation and its relationship with the socioeconomic characteristics of the producers. Remote sensing data of 2005 and 2010 was used to gauge the changes in forest area. Employing a probit model, we found that a forest coffee area being certified increased the probability of forest conservation by 19.3 percentage points relative to forest coffee areas lacking certification. We also found that although economically poor producers tended to engage in forest clearing, the forest coffee certification program had a significant impact on these producers. This result suggests that the certification program significantly affects the behaviors of economically poor producers and motivates these producers to conserve the forest. -- Highlights: • We employed the probit mode to evaluate the impact of the shade coffee certification on forest conservation in Ethiopia. • We estimated how the impact of the certification varied among producers with different characteristics. • The certification increased the probability of conserving forest by 19.3 percentage points. • Certification program motivated the economically poor producers to conserve the forest.
54 ENVIRONMENTAL SCIENCES↗
The theory behind, and the challenges of, conserving nature's stage in a time of rapid change
Most conservation planning to date has focused on protecting today's biodiversity with the assumption that it will be tomorrow's biodiversity. However, modern climate change has already resulted in distributional shifts of some species and is projected to result in many more shifts in the coming decades. As species redistribute and biotic communities reorganize, conservation plans based on current patterns of biodiversity may fail to adequately protect species in the future. One approach for addressing this issue is to focus on conserving a range of abiotic conditions in the conservation-planning process. By doing so, it may be possible to conserve an abiotically diverse "stage" upon which evolution will play out and support many actors (biodiversity). We reviewed the fundamental underpinnings of the concept of conserving the abiotic stage, starting with the early observations of von Humboldt, who mapped the concordance of abiotic conditions and vegetation, and progressing to the concept of the ecological niche. We discuss challenges posed by issues of spatial and temporal scale, the role of biotic drivers of species distributions, and latitudinal and topographic variation in relationships between climate and landform. For example, abiotic conditions are not static, but change through time-albeit at different and often relatively slow rates. In some places, biotic interactions play a substantial role in structuring patterns of biodiversity, meaning that patterns of biodiversity may be less tightly linked to the abiotic stage. Furthermore, abiotic drivers of biodiversity can change with latitude and topographic position, meaning that the abiotic stage may need to be defined differently in different places. Lastly, we conclude that protecting a diversity of abiotic conditions will likely best conserve biodiversity into the future in places where abiotic drivers of species distributions are strong relative to biotic drivers, where the diversity of abiotic settings will be conserved through time, and where connectivity allows for movement among areas providing different abiotic conditions.
54 ENVIRONMENTAL SCIENCES↗
Conservation management and ecosystem services in midwestern United States agricultural systems
The recognition that agricultural systems provide services beyond food production has motivated federal legislation and associated programs that promote sustainable management and conservation of productive working lands. This study evaluates the ability of the USDA Natural Resources Conservation Service's (NRCS) Conservation Measurement Tool (CMT), which has been used to determine eligibility for enrollment in the Conservation Stewardship Program, to reflect changes in ecosystem services resulting from the use of conservation management practices on croplands. This work evaluates four macroconcerns or outcomes (soil erosion, soil quality, water quality, and air quality) that are quantified within the tool by comparing CMT scores tabulated according to practices reported by farmers involved in grain producing operations in the US Midwest with soil health measures (dynamic soil properties [DSPs]) determined on 72 Illinois farm fields. Three management practice categories-Conventional, Conservation, and Organic-were evaluated. The CMT identified significant differences among management categories, and scores ranked consistently higher for Organic than Conventional or Conservation systems. Direct analysis of DSPs suggested that there were relatively small differences among soil health indicators measured on farms under varied management; this implies that the CMT might be overemphasizing the influence of selected management practices. The evaluation of multivariate relationships between the practices scored in the CMT and DSPs revealed that soil properties like soil pH and particulate organic matter-carbon (POM-C) can be used to improve the accuracy of the tool. They also show how relationships between questions (practices) and outcomes suggested by DSPs vary among farming categories and suggest this type of practice-based tool should be adapted by embedding factors to scale farming systems or, preferably, by adding questions that better describe important factors (e.g., plant productivity and fertilizer timing, rate, and form of application) and their interactions with other factors known to influence specific outcomes. This work shows how field data describing practices, properties, and outcomes can be used to statistically evaluate and refine conservation scoring tools.
conservation measurement tool↗
Global meta-analyses show that conservation tillage practices promote soil fungal and bacterial biomass
Despite a large number of published studies, a consensus has not been reached on how soil fungal and bacterial biomass, the primary regulators for soil organic matter decomposition, respond to conservation tillage, i.e., no or reduced tillage with >30 % residue covers. In this study we conducted a global meta-analysis of 60 studies to investigate the effects of conservation versus conventional tillage on soil fungal and bacterial biomass, fungal-to-bacterial ratios, and their relationship to other soil properties. Our results showed that conservation tillage greatly increased overall soil microbial biomass (37 %), including both fungal (31 %) and bacterial biomass (11 %), especially in top 20-cm soils or no-till agro-ecosystems, but conservation tillage effects were non-significant in sandy soils. Regardless of soil depth and tillage intensity, fungal-to-bacterial ratios did not greatly increase in conservation tillage scenarios, but were significantly affected by soil texture. Conservation tillage was also associated with significant increases in soil total C and N, and reduced soil pH. Increases in soil total C were positively associated with both fungal and bacterial biomass increases. Years under conservation tillage, time between last convention tillage to soil sampling, may indirectly affect fungal and bacterial biomass through soil C accumulation. Finally, our meta-analysis demonstrates that soil fungi and bacteria both respond positively to conservation tillage and are significantly associated with soil C content increase.
59 BASIC BIOLOGICAL SCIENCES↗
Using a Multi‐Institutional Ensemble of Watershed Models to Assess Agricultural Conservation Effectiveness in a Future Climate
This study investigates the combined impacts of climate change and agricultural conservation on the magnitude and uncertainty of nutrient loadings in the Maumee River Watershed, the second-largest watershed of the Laurentian Great Lakes. Two scenarios — baseline agricultural management and increased agricultural conservation — were assessed using an ensemble of five Soil and Water Assessment Tools driven by six climate models. The increased conservation scenario included raising conservation adoption rates from a baseline of existing conservation practices to feasible rates in the near future based on farmer surveys. This increased adoption of winter cover crops on 6%–10% to 60% of cultivated cropland; subsurface placement of phosphorus fertilizers on 35%–60% to 68% of cultivated cropland; and buffer strips intercepting runoff from 29%–34% to 50% of cultivated cropland. Increased conservation resulted in statistically significant (p ≤ 0.05) reductions in annual loads of total phosphorus (41%), dissolved reactive phosphorus (18%), and total nitrogen (14%) under the highest emission climate scenario (RCP 8.5). While nutrient loads decreased with increased conservation relative to baseline management for all watershed models, different conclusions on the true effectiveness of conservation under climate change may be drawn if only one watershed model was used.
54 ENVIRONMENTAL SCIENCES↗
A consistent and conservative Phase-Field method for multiphase incompressible flows
In the present study, a consistent and conservative Phase-Field method, including both the model and scheme, is developed for multiphase flows with an arbitrary number of immiscible and incompressible fluid phases. The consistency of mass conservation and the consistency of mass and momentum transport are implemented to address the issue of physically coupling the Phase-Field equation, which locates different phases, to the hydrodynamics. These two consistency conditions, as illustrated, provide the “optimal” coupling because (i) the new momentum equation resulting from them is Galilean invariant and implies the kinetic energy conservation, regardless of the details of the Phase-Field equation, and (ii) failures of satisfying the second law of thermodynamics or the consistency of reduction of the multiphase flow model only result from the same failures of the Phase-Field equation but are not due to the new momentum equation. Physical interpretation of the consistency conditions and their formulations are first provided, and general formulations that are obtained from the consistency conditions and independent of the interpretation of the velocity are summarized. Then, the present consistent and conservative multiphase flow model is completed by selecting a reduction consistent Phase-Field equation. Several novel techniques are developed to inherit the physical properties of the multiphase flows after discretization, including the gradient-based phase selection procedure, the momentum conservative method for the surface force, and the general theorems to preserve the consistency conditions on the discrete level. Equipped with those novel techniques, a consistent and conservative scheme for the present multiphase flow model is developed and analyzed. The scheme satisfies the consistency conditions, conserves the mass and momentum, and assures the summation of the volume fractions to be unity, on the fully discrete level and for an arbitrary number of phases. All those properties are numerically validated. Finally, numerical applications demonstrate that the present model and scheme are robust and effective in studying complicated multiphase dynamics, especially for those with large-density ratios.
97 MATHEMATICS AND COMPUTING↗
Exactly energy conserving semi-implicit particle in cell formulation
We report a new particle in cell (PIC) method based on the semi-implicit approach. The novelty of the new method is that unlike any of its semi-implicit predecessors at the same time it retains the explicit computational cycle and conserves energy exactly. Recent research has presented fully implicit methods where energy conservation is obtained as part of a non-linear iteration procedure. The new method (referred to as Energy Conserving Semi-Implicit Method, ECSIM), instead, does not require any non-linear iteration and its computational cycle is similar to that of explicit PIC. The properties of the new method are: i) it conserves energy exactly to round-off for any time step or grid spacing; ii) it is unconditionally stable in time, freeing the user from the need to resolve the electron plasma frequency and allowing the user to select any desired time step; iii) it eliminates the constraint of the finite grid instability, allowing the user to select any desired resolution without being forced to resolve the Debye length; iv) the particle mover has a computational complexity identical to that of the explicit PIC, only the field solver has an increased computational cost. The new ECSIM is tested in a number of benchmarks where accuracy and computational performance are tested. - Highlights: • We present a new fully energy conserving semi-implicit particle in cell (PIC) method based on the implicit moment method (IMM). The new method is called Energy Conserving Implicit Moment Method (ECIMM). • The novelty of the new method is that unlike any of its predecessors at the same time it retains the explicit computational cycle and conserves energy exactly. • The new method is unconditionally stable in time, freeing the user from the need to resolve the electron plasma frequency. • The new method eliminates the constraint of the finite grid instability, allowing the user to select any desired resolution without being forced to resolve the Debye length. • These features are achieved at a reduced cost compared with either previous IMM or fully implicit implementation of PIC.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Further adoption of conservation tillage can increase maize yields in the western US Corn Belt
Conservation tillage can reduce soil erosion, increase soil health, and decrease labor and fuel input costs. Despite these benefits, potential yield impacts remain an important concern for farmers considering adoption. Previous research suggests that conservation tillage is likely to have the largest yield benefits in more arid conditions, but a lack of field-level analyses across climatic, management and soil conditions limits confidence in such predictions. Satellite imagery provides the opportunity to monitor agricultural lands at sub-field resolution across large spatial scales and wide environmental gradients. Here we investigate the maize yield impacts of conservation tillage in the semi-arid western US Corn Belt, using sub-field resolution datasets on tillage practices and crop yields derived from satellite data spanning four states (Nebraska, Kansas, South Dakota, and North Dakota) between 2008 and 2020. On these datasets, we estimate heterogenous yield outcomes for several thousand maize fields across gradients in climate, soil quality and irrigation status by using a causal forests analysis, an adaptation of the random forests machine-learning algorithm for causal inference on observational data. We find that long-term adoption of conservation tillage increased rainfed maize yields by an average of 9.9% in the region. Impacts on irrigated yields were small and not statistically significant. These results, along with an analysis of variables related to greater than average yield benefits, indicate that improved water infiltration and retention are the primary reasons for conservation tillage benefits. Despite yield benefits, many fields estimated to see increased yields under long term low till have not adopted the practice. Therefore, we identify specific counties likely to benefit most from increased levels of adoption. Our results strengthen the understanding of the impacts of conservation agriculture on crop yields and help define environments and counties most likely to benefit from conservation tillage.
54 ENVIRONMENTAL SCIENCES↗