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Chen, Feng

Publications and source records attributed to Chen, Feng.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Direct flue gas capture for algae cultivation and subsequent valorization: evaluating life cycle emissions and costs

Algae cultivation and processing is an important pathway under discussion within the broader CO 2 capture and utilization umbrella. Here, we discuss the results of a life-cycle analysis and techno-economic analysis of a pilot-scale photobioreactor that uses flue gas directly from natural gas or biogas combustion at 3–5% CO 2 concentration. The system requires minimal freshwater use as it has been successfully run with industrial wastewater and has a much smaller areal footprint compared with open pond cultivation. Introducing the flue gas directly to the photobioreactor avoids the need for CO 2 separation and pressurization, which is undertaken in many other algae cultivation systems. For the end-use of the biomass, the default case assumes conversion of algae to liquid fuels via hydrothermal liquefaction. The results indicate that the pilot-scale system has a higher cost, and comparable greenhouse gas emissions compared to pond-based systems, especially as the grid is anticipated to evolve to a lower carbon intensity. The costs of algae biofuel production range from $\$12–16$ per GGE at the current pilot scale. Depending on whether the source of the carbon is fossil or biogenic, the net emissions are 68 g CO 2 e per MJ and −4 g CO 2 e per MJ respectively. If the marine algae species is used instead of the freshwater species, it offers an additional 16 g CO 2 e per MJ carbon fixation in the form of calcium carbonate. The findings point to broadly desirable trends in GHG emissions and costs, while the discussion aims to shed light on areas that could further improve the scalability of the system.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2024

Function and Evolution of the Plant MES Family of Methylesterases

Land plant evolution has been marked by numerous genetic innovations, including novel catalytic reactions. Plants produce various carboxyl methyl esters using carboxylic acids as substrates, both of which are involved in diverse biological processes. The biosynthesis of methyl esters is catalyzed by SABATH methyltransferases, and understanding of this family has broadened in recent years. Meanwhile, the enzymes catalyzing demethylation—known as methylesterases (MESs)—have received less attention. Here, we present a comprehensive review of the plant MES family, focusing on known biochemical and biological functions, and evolution in the plant kingdom. Thirty-two MES genes have been biochemically characterized, with substrates including methyl esters of plant hormones and several other specialized metabolites. One characterized member demonstrates non-esterase activity, indicating functional diversity in this family. MES genes regulate biological processes, including biotic and abiotic defense, as well as germination and root development. While MES genes are absent in green algae, they are ubiquitous among the land plants analyzed. Extant MES genes belong to three groups of deep origin, implying ancient gene duplication and functional divergence. Two of these groups have yet to have any characterized members. Much remains to be uncovered about the enzymatic functions, biological roles, and evolution of the MES family.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

AtDGCR14L contributes to salt-stress tolerance via regulating pre-mRNA splicing in Arabidopsis

In plants, the pre-mRNA alternative splicing has been demonstrated to be a crucial tier that regulates gene expression in response to salt stress. However, the underlying mechanisms remain elusive. Here, in this study, we studied the roles of DIGEORGE-SYNDROME CRITICAL REGION 14-like (AtDGCR14L) in regulating pre-mRNA splicing and salt stress tolerance. We discovered that Arabidopsis AtDGCR14L is required for maintaining plant salt stress tolerance and the constitutively spliced and active isoforms of important stress- and/or abscisic acid (ABA)-responsive genes. We also identified the interaction between AtDGCR14L and splicing factor U1-70k, which needs a highly conserved three amino acid (TWG) motif in DGCR14. Different from wild-type AtDGCR14L, the overexpression of TWG-substituted AtDGCR14L mutant did not change salt stress tolerance or pre-mRNA splicing of stress/ABA-responsive genes. Additionally, SWITCH3A (SWI3A) is a core subunit of the SWI/SUCROSE NONFERMENTING (SWI/SNF) chromatin-remodeling complexes. We found that SWI3A, whose splicing depends on AtDGCR14L, actively enhances salt stress tolerance. These results revealed that AtDGCR14L may play an essential role in crosstalk between plant salt-stress response and pre-mRNA splicing mechanisms. We also unveiled the potential role of SWI3A in controlling salt stress tolerance. The TWG motif in the intrinsically disordered region of AtDGCR14L is highly conserved and crucial for DGCR14 functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Multi-scale signaling and tumor evolution in high-grade gliomas

Although genomic anomalies in glioblastoma (GBM) have been well studied for over a decade, its 5-year survival rate remains lower than 5%. We seek to expand the molecular landscape of high-grade glioma, composed of IDH-wildtype GBM and IDH-mutant grade 4 astrocytoma, by integrating proteomic, metabolomic, lipidomic, and post-translational modifications (PTMs) with genomic and transcriptomic measurements to uncover multi-scale regulatory interactions governing tumor development and evolution. Applying 14 proteogenomic and metabolomic platforms to 228 tumors (212 GBM and 16 grade 4 IDH-mutant astrocytoma), including 28 at recurrence, plus 18 normal brain samples and 14 brain metastases as comparators, reveals heterogeneous upstream alterations converging on common downstream events at the proteomic and metabolomic levels and changes in protein-protein interactions and glycosylation site occupancy at recurrence. Recurrent genetic alterations and phosphorylation events on PTPN11 map to important regulatory domains in three dimensions, suggesting a central role for PTPN11 signaling across high-grade gliomas.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Emergent Superconductivity and Competing Charge Orders in Hole-Doped Square-Lattice t – J Model

The square-lattice Hubbard and closely related t-J models are considered as basic paradigms for understanding strong correlation effects and unconventional superconductivity (SC). Recent large-scale density matrix renormalization group simulations on the extended t-J model have identified d-wave SC on the electron-doped side (with the next-nearest-neighbor hopping t 2 > 0) but a dominant charge density wave (CDW) order on the hole-doped side (t 2 < 0), which is inconsistent with the SC of hole-doped cuprate compounds. We re-examine the ground-state phase diagram of the extended t-J model by employing the state-of-the-art density matrix renormalization group calculations with much enhanced bond dimensions, allowing more accurate determination of the ground state. On six-leg cylinders, while different CDW phases are identified on the hole-doped side for the doping range δ = 1/16 – 1/8, a SC phase emerges at a lower doping regime, with algebraically decaying pairing correlations and d-wave symmetry. On the wider eight-leg systems, the d-wave SC also emerges on the hole-doped side at the optimal 1=8 doping, demonstrating the winning of SC over CDW by increasing the system width. Furthermore, our results not only suggest a new path to SC in general t-J model through weakening the competing charge orders, but also provide a unified understanding on the SC of both hole- and electron-doped cuprate superconductors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Amorphous 1-D nanowires of calcium phosphate/pyrophosphate: A demonstration of oriented self-growth of amorphous minerals

Amorphous inorganic solids are traditionally isotropic, thus, it is believed that they only grow in a non-preferential way without the assistance of regulators, leading to the morphologies of nanospheres or irregular aggregates of nanoparticles. However, in the presence of (ortho)phosphate (Pi) and pyrophosphate ions (PPi) which have synergistic roles in biomineralization, the highly elongated amorphous nanowires (denoted ACPPNs) form in a regulator-free aqueous solution (without templates, additives, organics, etc). Based on thorough characterization and tracking of the formation process (e.g., Cryo-TEM, spherical aberration correction high resolution TEM, solid state NMR, high energy resolution monochromated STEM-EELS), the microstructure and its preferential growth behavior are elucidated. In ACPPNs, amorphous calcium orthophosphate and amorphous calcium pyrophosphate are distributed at separated but close sites. The ACPPNs grow via either the preferential attachment of ~2 nm nanoclusters in a 1-dimension way, or the transformation of bigger nanoparticles, indicating an inherent driving force-governed process. Here, we propose that the anisotropy of ACPPNs microstructure, which is corroborated experimentally, causes their oriented growth. This study proves that, unlike the conventional view, amorphous minerals can form via oriented growth without external regulation, demonstrating a novel insight into the structures and growth behaviors of amorphous minerals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Singlet, triplet, and pair density wave superconductivity in the doped triangular-lattice moiré system

Recent experimental progress has established the twisted bilayer transition metal dichalcogenide (TMD) as a highly tunable platform for studying many-body physics. Particularly, the homobilayer TMDs under displacement field are believed to be described by a generalized triangular-lattice Hubbard model with a spin-dependent hopping phase θ. To explore the effects of θ on the system, we perform density matrix renormalization group calculations for the relevant triangular lattice t-J model. By changing θ at small hole doping, we obtain a region of quasi-long-range superconducting order coexisting with charge and spin density wave within 0 < θ < π/3. The superconductivity is composed of a dominant spin singlet d-wave and a subdominant triplet p-wave pairing. Intriguingly, the S z = ±1 triplet pairing components feature pair-density waves. In addition, we find a region of triplet superconductivity coexisting with charge-density wave and ferromagnetism within π/3 < θ < 2π/3, which is related to the former phase at smaller θ by a combined operation of spin-flip and gauge transformation. Furthermore, our findings provide insights and directions for experimental search for exotic superconductivity in twisted TMD systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Identification of hidden N4-like viruses and their interactions with hosts

The N4-like viruses, which were recently assigned to the novel viral family Schitoviridae in 2021, belong to a podoviral-like viral lineage and possess conserved genomic characteristics and a unique replication mechanism. Despite their significance, our understanding of N4-like viruses is primarily based on viral isolates. To address this knowledge gap, this study has established a comprehensive N4-like viral data sets comprising 342 high-quality N4-like viruses/proviruses (144 viral isolates, 158 uncultured viruses, and 40 integrated N4-like proviruses). These viruses were classified into 97 subfamilies (89 of which are newly identified), 148 genera (100 of which are newly identified), and 253 species (177 of which are newly identified). The study reveals that N4-like viruses inhibit the polar region, oligotrophic open oceans, and the human gut, where they infect various bacterial lineages, such as Alpha/Beta/Gamma/Epsilon-proteobacteria in the Proteobacteria phylum. Although N4-like viral endogenization appears to be prevalent in Proteobacteria, it has also been observed in Firmicutes. Additionally, the phylogenetic analysis has identified evolutionary divergence within the hallmark genes of N4-like viruses, indicating a complex origin of the different conserved parts of viral genomes. Moreover, 1,101 putative auxiliary metabolic genes (AMGs) were identified in the N4-like viral pan-proteome, which mainly participate in nucleotide and cofactor/vitamin metabolisms. Of these AMGs, 27 were found to be associated with virulence, suggesting their potential involvement in the spread of bacterial pathogenicity. The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Activity of Brønsted Acid Sites in UiO-66 for Cyclohexanol Dehydration

Brønsted-acid sites are introduced via –OSO 3 H groups on the coordinatively unsaturated ZrO 2 nodes of UiO-66 metal organic frameworks (MOF). Such groups create strong Brønsted acidic sites that are active for cyclohexanol and ethanol dehydration (in liquid organic phase and gas phase, respectively). The intrinsic activity of Brønsted acid sites at nodes increased by increasing the concentration of sulfur, which is attributed to a shift from isolated µ 3 -OSO 3 H to two groups [(µ 3 -OSO 3 H) 2 ] interacting via hy-drogen bonding. For cyclohexanol dehydration, the relatively low activation enthalpies and negative transition entropies point to an E2 elimination mechanism, similar to dehydration with MFI zeolites in organic solvents. Furthermore, our results, show that the catalytic activity can be manipulated via the functionalization of zirconia nodes of the MOF framework.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Photoelectron spectroscopy with entangled photons; enhanced spectrotemporal resolution

In this theoretical study, we show how photoelectron signals generated by time-energy entangled photon pairs can monitor ultrafast excited state dynamics of molecules with high joint spectral and temporal resolutions, not limited by the Fourier uncertainty of classical light. This technique scales linearly, rather than quadratically, with the pump intensity, allowing the study of fragile biological samples with low photon fluxes. Since the spectral resolution is achieved by electron detection and the temporal resolution by a variable phase delay, this technique does not require scanning the pump frequency and the entanglement times, which significantly simplifies the experimental setup, making it feasible with current instrumentation. Application is made to the photodissociation dynamics of pyrrole calculated by exact nonadiabatic wave packet simulations in a reduced two nuclear coordinate space. This study demonstrates the unique advantages of ultrafast quantum light spectroscopy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma

Multiple myeloma (MM) is a highly refractory hematologic cancer. Targeted immunotherapy has shown promise in MM but remains hindered by the challenge of identifying specific yet broadly representative tumor markers. We analyzed 53 bone marrow (BM) aspirates from 41 MM patients using an unbiased, high-throughput pipeline for therapeutic target discovery via single-cell transcriptomic profiling, yielding 38 MM marker genes encoding cell-surface proteins and 15 encoding intracellular proteins. Of these, 20 candidate genes were highlighted that are not yet under clinical study, 11 of which were previously uncharacterized as therapeutic targets. The findings were cross-validated using bulk RNA sequencing, flow cytometry, and proteomic mass spectrometry of MM cell lines and patient BM, demonstrating high overall concordance across data types. Independent discovery using bulk RNA sequencing reiterated top candidates, further affirming the ability of single-cell transcriptomics to accurately capture marker expression despite limitations in sample size or sequencing depth. Target dynamics and heterogeneity were further examined using both transcriptomic and immuno-imaging methods. In summary, this study presents a robust and broadly applicable strategy for identifying tumor markers to better inform the development of targeted cancer therapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness

Clear cell renal cell carcinomas (ccRCCs) represent ∼75% of RCC cases and account for most RCC-associated deaths. Inter- and intratumoral heterogeneity (ITH) results in varying prognosis and treatment outcomes. To obtain the most comprehensive profile of ccRCC, we perform integrative histopathologic, proteogenomic, and metabolomic analyses on 305 ccRCC tumor segments and 166 paired adjacent normal tissues from 213 cases. Combining histologic and molecular profiles reveals ITH in 90% of ccRCCs, with 50% demonstrating immune signature heterogeneity. High tumor grade, along with BAP1 mutation, genome instability, increased hypermethylation, and a specific protein glycosylation signature define a high-risk disease subset, where UCHL1 expression displays prognostic value. Single-nuclei RNA sequencing of the adverse sarcomatoid and rhabdoid phenotypes uncover gene signatures and potential insights into tumor evolution. In vitro cell line studies confirm the potential of inhibiting identified phosphoproteome targets. This study molecularly stratifies aggressive histopathologic subtypes that may inform more effective treatment strategies.

CPTAC↗
DOE OSTI2022

Coherent ring-current migration of Mg-phthalocyanine probed by time-resolved X-ray circular dichroism

The coherent ring current of Mg-phthalocyanine created by a broad band UV-visible pump pulse shows variation with time, where the ring currents at the corner benzene rings, around the Mg cation and on the outer ring oscillate with different time periods and the current density migrates among these regions. The 7 pairs of E u degenerate excited states populated upon photoexcitation, generate 21 distinct coherent ring currents. We further calculate the time-resolved X-ray circular dichroism (TRXCD) spectrum of the coherences contributing to the ring current obtained by an attosecond X-ray probe pulse resonant with the nitrogen K-edge. A frequency domain TRXCD signal obtained by a Fourier transform of the signal with respect to the pump-probe delay time clearly separates the currents induced by different state pairs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Multifunctional transitional metal-based phosphide nanoparticles towards improved polysulfide confinement and redox kinetics for highly stable lithium-sulfur batteries

The shuttle effect and the sluggish redox kinetics of lithium polysulfides (LiPSs) are the major issues impeding the practical applications of lithium-sulfur batteries (LSBs). Herein, a highly-efficient Ni 2 P electrocatalyst supported on N, P co-doped graphene (Ni 2 P@NPG) is developed via a simple “recrystallization-self-assembly” method to address the above issues. Here, the ultrafine Ni 2 P nanoparticles ensure abundant adsorption-diffusion-conversion interfaces for accelerating LiPSs transformation and Li 2 S deposition, which extremely decreases the accumulation of LiPSs in the electrolyte and therefore prevents the migration of LiPSs. Their superior catalytic performance is demonstrated by reduced Gibbs free energy changes of rate-limiting step based on the systematic theoretical calculations and the reduced shuttle effect is tested by the three-dimensional reconstructions of Raman depth profiles. Benefiting from these synergistic effects, the LSBs with Ni 2 P@NPG modified separators present a superior cycling performance with an average capacity decay rate of 0.048 % per cycle at 1C around the 400 cycles and a high-rate capacity of 731 mAh/g at 2C. Even with a high-sulfur loading of 3.53 mg cm –2 , the cell can still contain a reversible capacity of 809 mAh/g at 0.2C with a remarkable columbic efficiency of 98.4 %.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Thousands of small, novel genes predicted in global phage genomes

Small genes (<150nucleotides) have been systematically overlooked in phage genomes. We employ a large scale comparative genomics approach to predict >40,000 small-gene families in 2.3 million phage genome contigs. We find that small genes in phage genomes are approximately 3-fold more prevalent than in host prokaryotic genomes. Our approach enriches for small genes that are translated in microbiomes, suggesting the small genes identified are coding. More than 9,000 families encode potentially secreted or transmembrane proteins, more than 5,000families encode predicted anti-CRISPR proteins, and more than500families encode predicted antimicrobial proteins. By combining homology and genomic-neighborhood analyses, we reveal substantial novelty and diversity within phage biology, including small phage genes found in multiple host phyla, small genes encoding proteins that play essential roles in host infection, and small genes that share genomic neighborhoods and whose encoded proteins may share related functions.

Fremin, Brayon↗