Engineering topics

Ding, Dian

Publications and source records attributed to Ding, Dian.

6 records

DOE OSTI2024

Diaminopurine in Nonenzymatic RNA Template Copying

In the RNA World before the emergence of an RNA polymerase, nonenzymatic template copying would have been essential for the transmission of genetic information. However, the products of chemical copying with the canonical nucleotides (A, U, C, and G) are heavily biased toward the incorporation of G and C, which form a more stable base pair than A and U. We therefore asked whether replacing adenine (A) with diaminopurine (D) might lead to more efficient and less biased nonenzymatic template copying by making a stronger version of the A:U pair. As expected, primer extension substrates containing D bound to U in the template more tightly than substrates containing A. However, primer extension with D exhibited elevated reaction rates on a C template, leading to concerns about fidelity. Our crystallographic studies revealed the nature of the D:C mismatch by showing that D can form a wobble-type base pair with C. We then asked whether competition with G would decrease the mismatched primer extension. We performed nonenzymatic primer extension with all four activated nucleotides on randomized RNA templates containing all four letters and used deep sequencing to analyze the products. We found that the DUCG genetic system exhibited a more even product distribution and a lower mismatch frequency than the canonical AUCG system. Furthermore, primer extension is greatly reduced following all mismatches, including the D:C mismatch. Our study suggests that D deserves further attention for its possible role in the RNA World and as a potentially useful component of artificial nonenzymatic RNA replication systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Unusual Base Pair between Two 2-Thiouridines and Its Implication for Nonenzymatic RNA Copying

2-Thiouridine (s 2 U) is a nucleobase modification that confers enhanced efficiency and fidelity both on modern tRNA codon translation and on nonenzymatic and ribozyme-catalyzed RNA copying. We have discovered an unusual base pair between two 2-thiouridines that stabilizes an RNA duplex to a degree that is comparable to that of a native A:U base pair. High-resolution crystal structures indicate similar base-pairing geometry and stacking interactions in duplexes containing s 2 U:s 2 U compared to those with U:U pairs. Notably, the C=O···H–N hydrogen bond in the U:U pair is replaced with a C=S···H–N hydrogen bond in the s 2 U:s 2 U base pair. The thermodynamic stability of the s 2 U:s 2 U base pair suggested that this self-pairing might lead to an increased error frequency during nonenzymatic RNA copying. However, competition experiments show that s 2 U:s 2 U base-pairing induces only a low level of misincorporation during nonenzymatic RNA template copying because the correct A:s 2 U base pair outcompetes the slightly weaker s 2 U:s 2 U base pair. In addition, even if an s 2 U is incorrectly incorporated, the addition of the next base is greatly hindered. This strong stalling effect would further increase the effective fidelity of nonenzymatic RNA copying with s 2 U. Our findings suggest that s 2 U may enhance the rate and extent of nonenzymatic copying with only a minimal cost in fidelity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Anthraquinone Flow Battery Reactants with Nonhydrolyzable Water-Solubilizing Chains Introduced via a Generic Cross-Coupling Method

Water-soluble anthraquinones (AQs) hold great promise serving as redox-active species in aqueous organic flow batteries. Systematic investigations into how the properties of redox molecules depend on the water-solubilizing groups (WSGs) and the way in which they are bound to the redox core are, however, still lacking. We introduce WSGs linked to anthraquinone by C=C bonds via a cross-coupling reaction and convert C=C to C–C bonds through hydrogenation. The anthraquinone and the WSGs are connected via (un)branched chains with (un)saturated bonds. We investigate the influence of chains and ionic ending groups on the redox potentials of the molecules and identify three important trends: (1) The electron-withdrawing ending groups can affect the redox potentials of AQs with two unsaturated hydrocarbons on the chains through π-conjugation. (2) For chains with two (un)saturated straight hydrocarbons, WSGs increase the redox potentials of the AQs in the order PO 3 2– < CO 2 – < SO 3 – . (3) AQs with (un)saturated chains at high pH possess desirably low redox potentials, high solubilities, and high stability. Disproportionation leads to the formation of anthrone, which can be regenerated to anthraquinone. Tautomerization results in the saturation of alkene chains, stabilizing the structure. Here, we utilize these observations to identify a potentially low-cost and long-lifetime negative electrolyte that demonstrates a temporal fade rate as low as 0.0128%/day when paired with a potassium ferrocyanide positive electrolyte.

25 ENERGY STORAGE↗

DOE OSTI2021

Role of emission controls in reducing the 2050 climate change penalty for PM2.5 in China

Previous studies demonstrated that global warming can lead to deteriorated air quality even when anthropogenic emissions were kept constant, which has been called a climate change penalty on air quality. It is expected that anthropogenic emissions will decrease significantly in the future considering the aggressive emission control actions in China. However, the dependence of climate change penalty on the choice of emission scenario is still uncertain. To fill this gap, we conducted multiple independent model simulations to investigate the response of PM2.5 to future (2050) climate warming (RCP8.5) in China but with different emission scenarios, including the constant 2015 emissions, the 2050 CLE emissions (based on Current Legislation), and the 2050 MTFR emissions (based on Maximum Technically Feasible Reduction). For each set of emissions, we estimate climate change penalty as the difference in PM2.5 between a pair of simulations with either 2015 or 2050 meteorology. Under 2015 emissions, we find a PM2.5 climate change penalty of 1.43 µg m-3 in Eastern China, leading to an additional 35,000 PM2.5-related premature deaths [95% confidence interval (CI), 21,000-40,000] by 2050. However, the PM2.5 climate change penalty weakens to 0.24 µg m-3 with strict anthropogenic emission controls under the 2050 MTFR emissions, which decreases the associated PM2.5-related deaths to 17,000. The smaller MTFR climate change penalty contributes 14% of the total PM2.5 decrease when both emissions and meteorology are changed from 2015 to 2050, and 24% of total health benefits associated with this PM2.5 decrease in Eastern China. This finding suggests that controlling anthropogenic emissions can effectively reduce the climate change penalty on PM2.5 and its associated premature deaths, even though a climate change penalty still occurs even under MTFR. Strengthened controls on anthropogenic emissions is key to attaining air quality targets and protecting human health in the context of future global climate change.

Liu, Song↗

DOE OSTI2020

Co-benefits of subnationally differentiated carbon pricing policies in China: Alleviation of heavy PM 2.5 pollution and improvement in environmental equity

Carbon policies differentiated according to regional disparities have been recognized and recommended. However, the air quality co-benefits of differentiated policies remain unclear. Here we combine a multi-regional dynamic computable general equilibrium (CGE) model and an extend response surface model (ERSM) to investigate the impact of nationally uniform and subnationally differentiated carbon pricing policies on fine particulate matter (PM 2.5 ) concentrations in China. All policies examined lead to the same accumulated national CO 2 emissions (2020–2050), with the 2030 emissions attaining China's national abatement target. We find that, when subnational policies differentiated according to provincial PM 2.5 concentrations are implemented, the higher-than-average carbon price over more polluted provinces results in twice as much reduction in CO 2 and air pollutant emissions in 2050 as the national policy. As a result, the subnational policies cause larger PM 2.5 concentration reductions in these provinces (9%–18%) than the national policy (7%–11%). Also, the subnational policies eliminate high PM 2.5 exposure of over 45 μg/m 3 which 12% people suffer from under the national policy. Overall, the subnational policies substantially reduce regional disparity in PM 2.5 pollution and hence improve environmental equity. The results suggest that subnationally differentiated carbon policies are a promising instrument to mitigate severe pollution and promote environmental equity.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2020

The quest for improved air quality may push China to continue its CO 2 reduction beyond the Paris Commitment

China is challenged with the simultaneous goals of improving air quality and mitigating climate change. The “Beautiful China” strategy, launched by the Chinese government in 2020, requires that all cities in China attain 35 μg/m 3 or below for annual mean concentration of PM 2.5 (particulate matter with aerodynamic diameter less than 2.5 μm) by 2035. Meanwhile, China adopts a portfolio of low-carbon policies to meet its Nationally Determined Contribution (NDC) pledged in the Paris Agreement. Previous studies demonstrated the co-benefits to air pollution reduction from implementing low-carbon energy policies. Pathways for China to achieve dual targets of both air quality and CO 2 mitigation, however, have not been comprehensively explored. Here, we couple an integrated assessment model and an air quality model to evaluate air quality in China through 2035 under the NDC scenario and an alternative scenario (Co-Benefit Energy [CBE]) with enhanced low-carbon policies. Results indicate that some Chinese cities cannot meet the PM 2.5 target under the NDC scenario by 2035, even with the strictest end-of-pipe controls. Achieving the air quality target would require further reduction in emissions of multiple air pollutants by 6 to 32%, driving additional 22% reduction in CO 2 emissions relative to the NDC scenario. Results show that the incremental health benefit from improved air quality of CBE exceeds 8 times the additional costs of CO 2 mitigation, attributed particularly to the cost-effective reduction in household PM 2.5 exposure. The additional low-carbon energy polices required for China’s air quality targets would lay an important foundation for its deep decarbonization aligned with the 2 °C global temperature target.

54 ENVIRONMENTAL SCIENCES↗