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At least 595 records · Page 33

Use Case Specification

Over the past three years, the Use Case Specification project has provided scenarios that have driven the development of key E-COMP capabilities and demonstrated their application to problems that the electric power industry is facing. These scenarios have provided the basis for which each Thrust has performed technical work, tying together E-COMP work under a common umbrella. Documented in this report is a summary of the background, motivations, and work – completed or proposed – under the three E-COMP use cases pursued to date: Offshore Wind, Remote Communities on the Olympic Peninsula, and Large Electric Loads.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Update on Model Specification Development of Ternary Pumped Storage Technologies [Slides]

T-PSH is an innovative structure of C-PSH that features two turbines, one for pumping and one for generation, replacing the single turbine in C-PSH. These turbines are housed in separate chambers, with an additional set of penstocks connecting the pump turbine to the hydraulic system. This structure enables T-PSH to operate in an HSC mode, allowing for simultaneous pumping and generation, which provides greater operational flexibility compared to C-PSH. To model T-PSH's HSC mode, a user defined turbine and governor system model is required, including the shared penstock model and additional pump turbine model. This specification will focus on the details of the user-defined turbine and governor model, which leverages the HYGOV model.

16 TIDAL AND WAVE POWER↗

GASNet-EX Specification Collection (Rev. 2024.5.0)

GASNet-EX is a portable, open-source, high-performance communication library designed to efficiently support the networking requirements of PGAS runtime systems and other alternative models in emerging exascale systems. It provides network-independent, high-performance communication primitives including Remote Memory Access (RMA) and Active Messages (AM). GASNet-EX is an evolution of the popular GASNet communication system, building upon over 20 years of lessons learned, and the primary goals are high performance, interface portability, and expressiveness. The library has been used to implement parallel programming models and libraries such as UPC, UPC++, Fortran coarrays, Legion, Chapel, and many others. This anthology collects together the four separate volumes that currently comprise the GASNet-EX specification, as of the 2024.5.0 release of GASNet-EX.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Produced Water DNA Database (PW-DNA): Utilizing KBase to generate an environmental specific curated molecular database

The deep subsurface is estimated to host the majority of Earth’s microbial biomass yet remains one of the most challenging environments to access and study. One common approach to investigate these microbial communities is through the analysis of produced water from subsurface reservoirs, where researchers can assess water and gas chemistry along with molecular (DNA/RNA) sequence data. Advances in high-throughput sequencing have greatly expanded our understanding of these environments and their biotechnological potential. However, further progress requires large-scale, integrative meta-analyses across diverse datasets. To address this need, we developed the Produced Water-DNA (PW-DNA) Database, a curated, publicly available resource that consolidates microbial DNA/RNA sequences, geochemical data, and relevant metadata from in situ hydrocarbon environments such as coal beds, oil reservoirs, and natural gas systems. The PW-DNA database delivers three core benefits to the research community: (1) it improves data sharing by linking environmental microbial datasets with corresponding geochemical parameters, enabling more robust filtering and analysis; (2) it connects with complementary research databases to promote broader dissemination and interoperability; and (3) it supports technological innovation by serving as a resource for identifying microbial trends and exploring genetic potential. While individual studies have highlighted basin-specific microbial communities and functional redundancy in biogeochemical cycling, a comprehensive, system-wide perspective is needed to better understand connectivity and novelty across subsurface ecosystems. By designing the PW-DNA in the KBase platform, we provide a reproducible, visual framework for integrating large-scale genomic and geochemical data, enabling researchers to perform more informed analyses and experimental design. Ultimately, this resource enhances the ability to identify, characterize, and interpret microbial functions across diverse subsurface environments, thereby accelerating discovery in subsurface microbiology and biotechnology.

59 BASIC BIOLOGICAL SCIENCES↗

Sensitivity of a Subject-specific Ankle Sprain Simulation to Extrinsic Versus Intrinsic Biomechanical Factors

Ankle sprains are the most common musculoskeletal injury in sport and military activity, despite existing prophylactic strategies. The purpose of this report was to develop a probabilistic simulation of lateral ankle sprains during single-limb drop landing, towards accelerating innovation in ankle sprain prevention. A deterministic, subject-specific musculoskeletal model was extended with automation and probabilistic distributions on sprain-related biomechanical factors. Probabilistic simulations were generated using traditional Monte Carlo techniques and the advanced mean value method, a more computationally-efficient approach. Predicted distributions of peak ankle joint rotations, velocities, and moments borne by supporting passive structures agreed favorably with the deterministic model and with reports of real sprain biomechanics. Parameter sensitivities identified that predictions were most strongly influenced by drop height, subtalar joint posture at contact, invertor/evertor co-activation, and passive ankle stiffness. The advanced mean value method predicted confidence bounds comparable to a 1000-trial Monte Carlo simulation, and required only 14 model evaluations and 4-min processing time. The extended probabilistic simulation may be useful to virtually test new prophylactic strategies for ankle sprains, and is made available for open-source use (https://simtk.org/projects/sprain-sim).

60 APPLIED LIFE SCIENCES↗

Transient histone deacetylase inhibition reveals cell type invariant and specific effects of chromatin decondensation on irradiation response

Radiation therapy plays a prominent role in breast cancer treatment, but the high doses of radiation damage both healthy and cancerous cells. Therefore, additional research is needed into combination therapies that could preferentially radiosensitize cancer cells compared to surrounding healthy tissue without causing deleterious side effects. Histone deacetylase inhibitor drugs (HDACis) have been tested as radiosensitizers in both basic research and clinical trials, but the long exposure time typically used in these treatments and the lack of matched healthy cell controls often leave aspects of their mechanism of action unclear. Here, we show that transient (2 h) trichostatin A (TSA) treatment of cancerous and non-tumorigenic breast epithelial cell lines increases immediate DNA damage and decreases long term cell viability in both cell types at high radiation doses. Transient TSA treatment also causes an increase in DNA damage signals after 5 Gy X-rays in other cancer and healthy cell types: A375 melanoma cells and BJ5-ta fibroblasts. This suggests that chromatin decompaction acts to increase cellular vulnerability to initial DNA damage from high doses of radiation in a cell type independent manner that does not rely on changes to DNA repair pathways caused by longer TSA treatment. However, responses to lower doses of radiation and long term survival are more cell type specific: only MCF7 cells experience an effect of TSA on DNA damage after 1 Gy X-ray radiation while MCF10a cells experience somewhat more evident cell viability effects of combined TSA and radiation treatment long term.

Li, Heng [Biochemistry & Cellular and Molecular Bi↗

Non-reactive facet specific adsorption as a route to remediation of chlorinated organic contaminants

The present work quantifies metal-contaminant interactions between palladium substrates and three salient chlorinated organic contaminants, namely trichloroethylene 1,3,5-trichlorobenzene (TCB), and 3,3′,4,4′-tetrachlorobiphenyl (PCB77). Given that Pd is one of the conventional catalytically active materials known for contaminant removal, maximizing catalytic efficiency through optimal adsorption dynamics reduces the cost of remediation of contaminants that are persistent water pollutants chronically affecting public health. Adsorption efficiency analyses from all-atom molecular dynamics (MD) simulations advance the understanding of reaction mechanisms available from density functional theory (DFT) calculations to an extractable feature scale that can fit the parametric design of supported metal catalytic systems and feed into high throughput catalyst selection. Data on residence time, site-specific adsorption, binding energies, packing geometries, orientation profiles, and the effect of adsorbate size show the anomalous behaviour of organic contaminant adsorption on the undercoordinated {110} surface as compared to the {111} and {100} surfaces. The intermolecular interaction within contaminants from molecular dynamics simulation exhibits refreshing results than ordinary single molecule density functional theory calculation. Since complete adsorption and dechlorination is an essential step for chlorinated organic contaminant remediation pathways, the presented profiles provide essential information for designing efficient remediation systems through facet-controlled palladium nanoparticles.

Guo, Hao↗

Characterizing the Influence of Organic Polymers on the Specific Reactivity of Particulate Remedial Amendments

Commercially available particulate amendments demonstrate high reactivity for effective treatment of water soluble organic and inorganic contaminants in laboratory studies; however, transport of these particles is constrained in the subsurface. In many field applications, particulate amendments are mixed with organic polymers to enhance mobility for direct push applications or stabilize suspensions for high mass loadings. As such, the interactions between particulate amendments, organic polymers and contaminant species need to be systematically investigated to properly understand mechanistic processes that facilitate predictive performance metrics for specific applications in situ . In this study, batch experiments were conducted to quantify the effects of organic polymers (xanthan gum, guar gum, and sodium alginate), polymer concentration (800 and 4,000 mg/L), and aging (up to 28 days) on chromate treatment rate and capacity by two classes of amendments: reductants [granular zero-valent iron (gZVI), micron-ZVI (mZVI), sulfur modified iron (SMI)], and an adsorbent (bismuth sub-nitrate). When particulate amendments were suspended in polymer solutions, reductants retained between 84–100% of the amendment treatment capacity. Conversely, the adsorbent maintained 63–97% relative treatment capacity of the no-polymer control. Polymer solutions had a more pronounced impact on the rate of chromate removal; first order rates of chemical reduction decreased by as much as 70% and adsorption by up to 81% relative to the no-polymer controls. Polymer–amendment aging experiments also showed decreased Cr(VI) treatment capacity; reductants decreased by as much as 24% and adsorption decreased by as much as 44% after 28 days of incubation. While polymer suspensions are needed to aid the injection of particulate amendments into the subsurface, the results from this study indicate potential losses of treatment capacity and a decrease in the rate of remedial performance due to the physical and chemical interactions between polymer suspensions and reactive particulate amendments. Simple batch systems provide baseline characterization of tripartite interactions for the removal of Cr(VI). Additional work is needed to quantify the full impact of polymers on remedial outcomes under site relevant conditions at field scale.

54 ENVIRONMENTAL SCIENCES↗

Metagenomics Reveals Diet-Specific Specialization of Bacterial Communities in Fungus Gardens of Grass- and Dicot-Cutter Ants

Leaf-cutter ants in the genus Atta are dominant herbivores in the Neotropics. While most species of Atta cut dicots to incorporate into their fungus gardens, some species specialize on grasses. Here we examine the bacterial community associated with the fungus gardens of grass- and dicot-cutter ants to examine how changes in substrate input affect the bacterial community. We sequenced the metagenomes of 12 Atta fungus gardens, across four species of ants, with a total of 5.316 Gbp of sequence data. We show significant differences in the fungus garden bacterial community composition between dicot- and grass-cutter ants, with grass-cutter ants having lower diversity. Reflecting this difference in community composition, the bacterial functional profiles between the fungus gardens are significantly different. Specifically, grass-cutter ant fungus garden metagenomes are particularly enriched for genes responsible for amino acid, siderophore, and terpenoid biosynthesis while dicot-cutter ant fungus gardens metagenomes are enriched in genes involved in membrane transport. Differences between community composition and functional capacity of the bacteria in the two types of fungus gardens reflect differences in the substrates that the ants incorporated. These results show that different substrate inputs matter for fungus garden bacteria and shed light on the potential role of bacteria in mediating the ants’ transition to the use of a novel substrate.

59 BASIC BIOLOGICAL SCIENCES↗

Diabetes-specific formula with standard of care improves glycemic control, body composition, and cardiometabolic risk factors in overweight and obese adults with type 2 diabetes: results from a randomized controlled trial

Background and aims Medical nutrition therapy is important for diabetes management. This randomized controlled trial investigated the effects of a diabetes-specific formula (DSF) on glycemic control and cardiometabolic risk factors in adults with type 2 diabetes (T2D). Methods Participants ( n = 235) were randomized to either DSF with standard of care (SOC) (DSF group; n = 117) or SOC only (control group; n = 118). The DSF group consumed one or two DSF servings daily as meal replacement or partial meal replacement. The assessments were done at baseline, on day 45, and on day 90. Results There were significant reductions in glycated hemoglobin (−0.44% vs. –0.26%, p = 0.015, at day 45; −0.50% vs. −0.21%, p = 0.002, at day 90) and fasting blood glucose (−0.14 mmol/L vs. +0.32 mmol/L, p = 0.036, at day 90), as well as twofold greater weight loss (−1.30 kg vs. –0.61 kg, p < 0.001, at day 45; −1.74 kg vs. –0.76 kg, p < 0.001, at day 90) in the DSF group compared with the control group. The decrease in percent body fat and increase in percent fat-free mass at day 90 in the DSF group were almost twice that of the control group (1.44% vs. 0.79%, p = 0.047). In addition, the percent change in visceral adipose tissue at day 90 in the DSF group was several-fold lower than in the control group (−6.52% vs. –0.95%, p < 0.001). The DSF group also showed smaller waist and hip circumferences, and lower diastolic blood pressure than the control group (all overall p ≤ 0.045). Conclusion DSF with SOC yielded significantly greater improvements than only SOC in glycemic control, body composition, and cardiometabolic risk factors in adults with T2D.

Tey, Siew Ling↗

Opening Up Transactive Systems: Introducing TESS and Specification in a Field Deployment

Transactive energy systems (TS) use automated device bidding to access (residential) demand flexibility and coordinate supply and demand on the distribution system level through market processes. In this work, we present TESS, a modularized platform for the implementation of TS, which enables the deployment of adjusted market mechanisms, economic bidding, and the potential entry of third parties. TESS thereby opens up current integrated closed-system TS, allows for the better adaptation of TS to power systems with high shares of renewable energies, and lays the foundations for a smart grid with a variety of stakeholders. Furthermore, despite positive experiences in various pilot projects, one hurdle in introducing TS is their integration with existing tariff structures and (legal) requirements. In this paper, we therefore describe TESS as we have modified it for a field implementation within the service territory of Holy Cross Energy in Colorado. Importantly, our specification addresses challenges of implementing TS in existing electric retail systems, for instance, the design of bidding strategies when a (non-transactive) tariff system is already in place. We conclude with a general discussion of the challenges associated with “brownfield” implementation of TS, such as incentive problems of baseline approaches or long-term efficiency.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Conformer-Specific Dissociation Dynamics in Dimethyl Methylphosphonate Radical Cation

The dynamics of the dimethyl methylphosphonate (DMMP) radical cation after production by strong field adiabatic ionization have been investigated. Pump-probe experiments using strong field 1300 nm pulses to adiabatically ionize DMMP and a 800 nm non-ionizing probe induce coherent oscillations of the parent ion yield with a period of about 45 fs. The yields of two fragments, PO 2 C 2 H 7 + and PO 2 CH 4 + , oscillate approximately out of phase with the parent ion, but with a slight phase shift relative to each other. We use electronic structure theory and nonadiabatic surface hopping dynamics to understand the underlying dynamics. The results show that while the cation oscillates on the ground state along the P=O bond stretch coordinate, the probe excites population to higher electronic states that can lead to fragments PO 2 C 2 H 7 + and PO 2 CH 4 + . The computational results combined with the experimental observations indicate that the two conformers of DMMP that are populated under experimental conditions exhibit different dynamics after being excited to the higher electronic states of the cation leading to different dissociation products. These results highlight the potential usefulness of these pump-probe measurements as a tool to study conformer-specific dynamics in molecules of biological interest.

59 BASIC BIOLOGICAL SCIENCES↗

Specific Effect of Peculiar Velocities on Dark-energy Constraints from Type Ia Supernovae

Peculiar velocities of Type Ia supernova (SN Ia) host galaxies affect the dark-energy parameter constraints in a small but very specific way: the parameters are biased in a single direction in parameter space that is a priori knowable for a given SN Ia data set. We demonstrate the latter fact with a combination of inference from a cosmological N-body simulation with overwhelming statistics applied to the Pantheon SN Ia data set, then confirm it by simple quantitative arguments. Here, we quantify small modifications to the current analyses that would ensure that the effect of cosmological parameters is essentially guaranteed to be negligible.

79 ASTRONOMY AND ASTROPHYSICS↗

Combining Three-Dimensional Modeling with Artificial Intelligence to Increase Specificity and Precision in Peptide–MHC Binding Predictions

The reliable prediction of the affinity of candidate peptides for the MHC is important for predicting their potential antigenicity and thus influences medical applications, such as decisions on their inclusion in T cell–based vaccines. In this study, we present a rapid, predictive computational approach that combines a popular, sequence-based artificial neural network method, NetMHCpan 4.0, with three-dimensional structural modeling. We find that the ensembles of bound peptide conformations generated by the programs MODELLER and Rosetta FlexPepDock are less variable in geometry for strong binders than for low-affinity peptides. In tests on 1271 peptide sequences for which the experimental dissociation constants of binding to the well-characterized murine MHC allele H-2D b are known, by applying thresholds for geometric fluctuations the structure-based approach in a standalone manner drastically improves the statistical specificity, reducing the number of false positives. Furthermore, filtering candidates generated with NetMHCpan 4.0 with the structure-based predictor led to an increase in the positive predictive value (PPV) of the peptides correctly predicted to bind very strongly (i.e., Kd < 100 nM) from 40 to 52% (p = 0.027). The combined method also significantly improved the PPV when tested on five human alleles, including some with limited data for training. Overall, an average increase of 10% in the PPV was found over the standalone sequence-based method. The combined method should be useful in the rapid design of effective T cell–based vaccines.

60 APPLIED LIFE SCIENCES↗