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At least 181 records · Page 10

scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing

Abstract Single-cell ATAC-seq has emerged as a powerful approach for revealing candidate cis-regulatory elements genome-wide at cell-type resolution. However, current single-cell methods suffer from limited throughput and high costs. Here, we present a novel technique called scifi-ATAC-seq, single-cell combinatorial fluidic indexing ATAC-sequencing, which combines a barcoded Tn5 pre-indexing step with droplet-based single-cell ATAC-seq using the 10X Genomics platform. With scifi-ATAC-seq, up to 200,000 nuclei across multiple samples can be indexed in a single emulsion reaction, representing an approximately 20-fold increase in throughput compared to the standard 10X Genomics workflow.

59 BASIC BIOLOGICAL SCIENCES↗

Off-gas capture: a promising strategy for removal and recovery of toxic bioproducts in aerobic fermentation

In many bioprocesses, maximum achievable titers are limited below economically viable levels by toxic accumulation of the primary end-product. To combat end-product inhibition, a variety of in situ product removal technologies have been developed to selectively remove or partition toxic bioproducts, thereby prolonging fermentation and improving overall process efficiency. Use of an in situ organic overlay to partition toxic hydrophobic products is a commonly employed approach, but this technique occupies valuable space in the fermentor, imposes replacement costs for unrecovered solvent, and increases downstream separation due to formation of stable emulsions. In addition, for many volatile hydrophobic products produced under aerobic conditions—including medium-chain alcohols, esters, monoterpenes, and other aviation fuel precursors—a significant fraction of the product is volatilized to the fermentor off-gas and must be recovered separately to maximize product yield. To address these challenges, we explore the viability of leveraging existing aeration energy to fully strip and recover volatile products from the fermentor off-gas. We compare two strategies of in situ product removal—liquid–liquid extraction and direct recovery from fermentation off-gas—for the production and recovery of intermediates used to generate isoprene and DMCO (1,4-dimethylcyclooctane), a high-performance jet fuel. We evaluate product toxicity, solvent toxicity, solvent partitioning, and the impact of aeration and internal overlay configurations on product volatilization rates. We then optimize product recovery from fermentor off-gas via condensation in chilled solvent, achieving 84% capture efficiency. In addition to greatly simplifying downstream processing, relying on aeration for product volatilization in the absence of an internal overlay enables continuous removal of toxic fermentation products up to maximum isoprenol titers of 20.4 g/L, the highest reported to date.

isoprene↗

Novel Membrane and Electrodeposition-Based Separation and Recovery of Rare Earth Elements from Coal Combustion Residues (Final Report)

This project developed a hydrometallurgical-based technology to extract and concentrate rare earth elements (REEs) from a representative group of coal combustion residuals (CCRs) from major coal sources in the United States. The approach for REE recovery comprises two general components: (1) Leaching of REEs from CCRs and (2) Separation of REEs from other major ions in the CCR leachate. The leaching step entails acid leaching with nitric or hydrochloric acid, and in some cases, pretreatment of CCRs with alkaline roasting prior to acid leaching. The follow-up REE recovery steps involve a series of membrane-based methods to separate and concentrate rare earth ions from other major ions in acid leachates of CCRs. These methods include liquid emulsion membranes, supported liquid membranes and electrodeposition with carbon nanotube electrochemical filters. The advantage of these separation approaches (relative to conventional approaches such as solvent extraction) is a reduction in the usage of solvents and other costly chemicals and a reduction of hazardous waste products that are challenges in conventional REE separation methods. In the testing of our process, we selected a representative set of CCR samples from our collection and performed a suite of characterization measurements (total REE content and major mineralogy). The major results of this work demonstrated that heated acid leaching could efficiently extract REEs from PRB-based coal fly ashes while the Appalachian and Illinois Basin CCRs required alkaline roasting with NaOH prior to acid leaching at room temperature. The supported liquid membrane (SLM) configuration and electrochemical deposition (ED) system yielded the most promising methods of REE recovery from the acid leachates of fly ash. Our most concentrated product to date comprised 1 wt.% (dry basis) REEs produced from an Appalachian-based fly ash leached and purified by SLM. The SLM separation process was more selective for heavy REEs over the light REEs. When SLM was combined with ED, preliminary results demonstrated that a final product of >2 wt.% REEs was possible.

01 COAL, LIGNITE, AND PEAT↗

2022 American Conference on Neutron Scattering (ACNS 2022)

The 11th American Conference on Neutron Scattering (ACNS 2022) will be held on June 5-9, 2022, in Boulder, CO. The Conference will provide essential information on the breadth and depth of current neutron-related research worldwide. Hosted by the Neutron Scattering Society of America, this year’s Conference will feature a combination of invited and contributed talks, poster sessions, and tutorials. Topics of the conference are: Advances in Neutron Facilities, Instrumentation and Software: Developments in sources, instrumentation, sample environments and control software. Hard Condensed Matter: Magnetism, correlated metals, quantum/topological materials, superconductors, ferroelectrics, multiferroics, glasses, and disorder phenomena. Submissions outlining examples of neutron scattering in industrial and engineering applications involving hard condensed matter systems are also encouraged. Soft Matter: Neutron studies of soft materials and related fields including in situ and in operando studies. Polymers, surfactants, emulsions, gels, nanoparticles, colloidal suspensions and more. Submissions of computational studies or applications of machine learning beneficial to neutron scattering experiments, as well as examples of neutron scattering in industrial and engineering applications are strongly encouraged. Biology, Biophysics and Biotechnology: Neutron studies of biological and biologically relevant systems. Proteins, bio membranes, biological assemblies, natural materials, nucleic acids, drug-delivery platforms and biomedical systems. Submissions of computational studies or applications of machine learning beneficial to biological neutron scattering experiments, as well as examples of neutron scattering in applied research involving biological systems, are strongly encouraged. Materials Chemistry and Energy: Neutron-based studies of functional materials and materials for energy applications. Examples include porous materials such as metal organic frameworks (MOFs), zeolites; phosphors; novel pigments; electrolytes; catalysts; ionic conductors/cathode materials; photovoltaic materials (hybrid perovskites); thermoelectrics; magnetocalorics/electrocalorics. Structural Materials and Engineering: Neutron scattering studies of materials and engineering processes including structural materials, concrete and metals, as well as engineering processes including combustion, corrosion, additive manufacturing, and others. Neutron Physics: Fundamental physical studies of the neutron and related areas. Emerging Applications in Neutron Scattering: Machine Learning and Data Science: Advances in computing power have contributed to rapidly evolving machine learning and data science fields that can be leveraged to the benefit of the neutron scattering community. The purpose of this session is to highlight recent advances in machine learning and data science and to serve as the foundation of a parallel data and computation track highlighting computation advances and applications in neutron scattering throughout the conference.

36 MATERIALS SCIENCE↗

Design of functional materials based on new principles of disorder

The main goal of the project for many years was to study and understand the jamming transition and the properties of the marginally jammed state, and to apply that understanding to real systems, including atomic, molecular, metallic and polymeric glasses, colloidal suspensions, granular materials, foams and emulsions, as well as the dynamics of systems driven away from the static jammed state by applying temperature or strain. As we gained greater insight into the jamming problem, we applied it to other big problems that had not previously been recognized as being related to jamming, such as memory formation, metamaterials design and learning.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Observation of Antiproton Annihilation at Rest in LArIAT

Antiproton annihilation at-rest can provide a unique probe into the intra-nuclear structure of nuclei. This process was first observed in the 1950’s using photographic emulsion and has since been observed and studied on a variety of nuclei. We present here the first observation and reconstruction of antiproton annihilation at-rest interactions on argon nuclei using data from the LArIAT experiment, a liquid argon time projection chamber (LArTPC). LArIAT was exposed to a charged particle test-beam at Fermilab from 2015-2017. Antiprotons tagged using LArIAT’s beamline instrumentation were reconstructed in the LArTPC, and the multiplicities of final-state particles emerging from the identified annihilation at-rest vertex were measured. These results will inform searches for neutron-antineutron oscillation events in the future LArTPCs like DUNE due to their similar topological signature.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Simulation of Particulate Transport for Delivery of Solid Amendments into the Subsurface: FY24 Status Report

For particulate-based amendments to be viable for field-scale remediation at the Hanford Site (e.g., 200 DV-1 Operable Unit), particles need to be delivered a sufficient radial distance from an injection well and retained at concentrations high enough for effective treatment. An accurate description of the particle radius of influence (ROI) is critical for developing an overall remediation strategy. However, field-scale particle simulations are currently limited due to insufficient simulation capabilities and a lack of experimental data to validate and parameterize particle transport models. To help build toward field-scale deployment, this fiscal year (FY) we have (1) developed a pre screening tool to estimate particle transport, (2) implemented particle transport models within PFLOTRAN, and (3) conducted preliminary estimations of particle ROI. While field-scale numerical simulations will ultimately be necessary before remedy design and field implementation, we have developed a pre-screening tool that offers valuable estimations of expected particle injectability and ROI in a 1-D system. The advantage of the tool is that it does not require extensive laboratory experiments and instead makes predictions based solely on routine laboratory measurements. This tool can assist in down-selection and decision-making by identifying which particle amendment systems are worth pursuing in future laboratory experiments, such as 1-D column tests and beyond. With any system, scaling up from the lab to the field presents challenges. Currently, there is no field data available for model calibration or validation. However, the theoretical particle models being developed herein are the best tools available to guide progress toward field deployment. To help bridge this gap and verify model predictions, larger-scale lab experiments are being proposed. To advance simulation capabilities, six particle transport models are being integrated into the reactive transport simulator PFLOTRAN. These include colloid filtration theory (CFT) and five additional particle transport models (M1-M5). Each model, from M1 to M5, progressively incorporates additional particle transport and retention processes. Ultimately, the simplest model capable of accurately describing 1-D column data will be selected and parameterized. During FY24, the CFT and M1 model have been fully implemented within PFLOTRAN. Using an existing 1 D column experiment, the two currently implemented particle transport models (CFT and M1), and associated parameters, were fit to this experiment. While simpler model formulations are helpful for estimations, these formulations could not fully describe particle transport and retention behavior in the previous 1-D column experiment. Thus, additional complexities will need to be considered, which will be accounted for in the M2-M5 model formulations. Additionally, because a viscous, shear thinning fluid was required to keep particles in suspension, considerations for flow will also need to also be accounted for. Therefore, a new immiscible two-phase flow mode is currently being implemented in PFLOTRAN. With some modifications, this new flow module could also support simulation of non-Newtonian liquid amendments, foams, and emulsions. We also estimated the expected ROI of solid amendments using 1-D simulations. The average predicted ROI was approximately 15 ft for micron-sized zero valent iron (mZVI) suspended in xanthan gum (XG). Using the pre screening tool and ROI estimates, additional amendment-delivery laboratory characterization and experiments are proposed. The results from additional experiments can be used to validate and parametrize particulate transport model formulations, which will ultimately provide predictive capabilities for field amendment-delivery systems.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Effect of Polyphenylsulfone and Polysulfone Incompatibility on the Structure and Performance of Blend Membranes for Ultrafiltration

This study deals with the modification of polyphenylsulfone ultrafiltration membranes by introduction of an incompatible polymer polysulfone to the polyphenylsulfone casting solution to improve the permeability. The correlation between properties of the blend polyphenylsulfone/polysulfone solutions and porous anisotropic membranes for ultrafiltration prepared from these solutions was revealed. The blend polyphenylsulfone/polysulfone solutions were investigated using a turbidity spectrum method, optical microscopy and measurements of dynamic viscosity and turbidity. The structure of the prepared blend flat sheet membranes was studied using scanning electron microscopy. Membrane separation performance was investigated in the process of ultrafiltration of human serum albumin buffered solutions. It was found that with the introduction of polysulfone to the polyphenylsulfone casting solution in N-methyl-2-pyrrolidone the size of supramolecular particles significantly increases with the maximum at (40–60):(60:40) polyphenylsulfone:polysulfone blend ratio from 76 nm to 196–354 nm. It was shown that polyphenylsulfone/polysulfone blend solutions, unlike the solutions of pristine polymers, are two-phase systems (emulsions) with the maximum droplet size and highest degree of polydispersity at polyphenylsulfone/polysulfone blend ratios (30–60):(70–40). Pure water flux of the blend membranes passes through a maximum in the region of the most heterogeneous structure of the casting solution, which is associated with the imposition of a polymer-polymer phase separation on the non-solvent induced phase separation upon membrane preparation. The application of polyphenylsulfone/polysulfone blends as membrane-forming polymers and polyethylene glycol (Mn = 400 g·mol -1 ) as a pore-forming agent to the casting solutions yields the formation of ultrafiltration membranes with high membrane pure water flux (270 L·m -2 ·h -1 at 0.1MPa) and human serum albumin rejection of 85%.

36 MATERIALS SCIENCE↗

Balancing Functionality and Printability: High-Loading Polymer Resins for Direct Ink Writing

Although direct ink writing (DIW) allows the rapid fabrication of unique 3D printed objects, the resins—or “inks”—available for this technique are in short supply and often offer little functionality, leading to the development of new, custom inks. However, when creating new inks, the ability of the ink to lead to a successful print, or the “printability,” must be considered. Thus, this work examined the effect of filler composition/concentration, printing parameters, and lattice structure on the printability of new polysiloxane inks incorporating high concentrations (50–70 wt%) of metallic and ceramic fillers as well as emulsions. Results suggest that strut diameter and spacing ratio have the most influence on the printability of DIW materials and that the printability of silica- and metal-filled inks is more predictable than ceramic-filled inks. Additionally, higher filler loadings and SC geometries led to stiffer printed parts than lower loadings and FCT geometries, and metal-filled inks were more thermally stable than ceramic-filled inks. The findings in this work provide important insights into the tradeoffs associated with the development of unique and/or multifunctional DIW inks, printability, and the final material’s performance.

36 MATERIALS SCIENCE↗

A Pentavalent HIV-1 Subtype C Vaccine Containing Computationally Selected gp120 Strains Improves the Breadth of V1V2 Region Responses

Background: HIV-1 envelope (Env) variable loops 1 and 2 (V1V2) directed non-neutralizing antibodies were a correlate of decreased transmission risk in the RV144 vaccine trial. Thus, the elicitation and breadth of antibody responses against the V1V2 of HIV-1 Env are important considerations for HIV-1 vaccine candidates. The V1V2 region’s highly variable nature and the extensive diversity of subtype C HIV-1 Envelopes (Envs) make the V1V2 response breadth a high priority for HIV-1 vaccine regimens aiming for V1V2-mediated protection in Southern Africa. Here, we determined whether the breadth of the anti-V1V2 vaccine response can be broadened by including HIV-1 Env strains computationally designed to enhance the coverage of subtype C V1V2 sequence diversity. Methods: Three subtype C Env strains were selected to maximize antibody binding coverage while complementing subtype C vaccine gp120s that were given in human clinical trials in South Africa, as well as to improve epitope accessibility. Humoral immunogenicity of a novel trivalent gp120 vaccine immunogen, a bivalent gp120 boost already in clinical trials (1086C and TV1), and a pentavalent (all five gp120s combined) were evaluated in a preclinical immunization study in guinea pigs. The pentavalent combination was further evaluated with alum versus glucopyranosyl lipid adjuvants formulated in squalene-in-water emulsion (GLA-SE) adjuvants in non-human primates. The breadth of the anti-V1V2 response was assessed using an array of cross-subtype variable loops 1&2 (V1V2) scaffold proteins and linear V2 peptides. Results: The breadth of the IgG response against V1V2 antigens of the trivalent and pentavalent groups was comparable, and both were greater than the breadth of the bivalent group. Linear epitope mapping showed that two linear epitopes in V2 were targeted by the vaccinated animals: the V2 hotspot focused at 169K that potentially correlated with decreased HIV-1 risk in RV144 and the V2.2 site (179LDV/I181) that is part of the integrin α4β7 binding site. The bivalent vaccine elicited a significantly higher magnitude of binding to the V2 hotspot compared to the trivalent vaccine whereas the trivalent vaccine elicited significantly higher binding to the V2.2 epitope compared to the bivalent vaccine, while the pentavalent recognized both regions. Conclusions: These results demonstrate that the three new computationally selected subtype C Envs successfully complemented 1086C and TV1 for broader V1V2 antibody responses, and, in concert with adjuvants that stimulate V1V2 responses, can be considered as part of a rationale immunogen design to improve V1V2 IgG coverage in future vaccine trials in South Africa.

Immunology↗

Piezocatalytic ZnS:Mn 2+ Nanocrystals for Enhanced Organic Dye Degradation

Piezocatalysis, an emerging approach that harnesses mechanical energy to drive chemical reactions, has garnered significant attention due to its potential applications in diverse fields, particularly in environmental remediation. Its broader application, however, is often hindered by the low efficiency of existing piezocatalytic materials. Here, we report the synthesis of Mn 2+ -doped ZnS nanocrystals with improved piezoelectric properties using an emulsion-based colloidal assembly technique. Through well-controlled Mn 2+ doping, these nanocrystals demonstrate high piezocatalytic activity for degrading organic dyes under ultrasonic vibration. The optimal performance is achieved with 3% Mn 2+ doping, outperforming many existing piezocatalysts. Mechanistic studies reveal the generation of reactive oxygen species as the primary driving force for degradation. Notably, pre-excitation with UV light further boosts the piezocatalytic efficiency of these metal ion-doped ZnS nanocrystals by filling electron trap states, leading to improved overall performance. This research paves the way for developing high-performance piezocatalysts, expanding the potential of piezocatalysis for a wide range of applications.

36 MATERIALS SCIENCE↗

Surfactant for enhanced oil recovery

A Janus graphene nanosheet (JGN) surfactant formed from a two-dimensional graphene oxide sheet and functionalized to produce an amphiphilic graphene nanosheet. The JGN may be a component of a nanofluid utilized in nanofluid flooding for oil recovery. The JGN may also be used as solid surfactants to form emulsions for oil recovery.

Ren, Zhifeng↗

Systems and processes for recovery of high-grade rare earth concentrate from acid mine drainage

In one aspect, the disclosure relates to a continuous process for treating acid mine drainage while simultaneously recovering a high-grade rare earth preconcentrate suitable for extraction of commercially valuable rare earth oxides. In a further aspect, the preconcentrate is from about 0.1% to 5% rare earth elements on a dry weight basis. In another aspect, the disclosure relates to a method for processing the preconcentrate to generate a pregnant leach solution that does not form gels or emulsions and is suitable for processing via solvent extraction. In another aspect, the disclosure relates to a system and plant for carrying out the disclosed process. In still another aspect, the disclosure relates to a composition containing rare earth elements produced by the process disclosed herein. This abstract is intended as a scanning tool for purposes of searching in the particular art and is not intended to be limiting of the present disclosure.

Ziemkiewicz, Peter F.↗

Acid-degradable and bioerodible modified polyhydroxylated materials

Compositions and methods of making a modified polyhydroxylated polymer comprising a polyhydroxylated polymer having reversibly modified hydroxyl groups, whereby the hydroxyl groups are modified by an acid-catalyzed reaction between a polydroxylated polymer and a reagent such as acetals, aldehydes, vinyl ethers and ketones such that the modified polyhydroxylated polymers become insoluble in water but freely soluble in common organic solvents allowing for the facile preparation of acid-sensitive materials. Materials made from these polymers can be made to degrade in a pH-dependent manner. Both hydrophobic and hydrophilic cargoes were successfully loaded into particles made from the present polymers using single and double emulsion techniques, respectively. Due to its ease of preparation, processability, pH-sensitivity, and biocompatibility, of the present modified polyhydroxylated polymers should find use in numerous drug delivery applications.

Frechet, Jean M. J.↗

Synthesis and Characterization of Polymeric Pore Former Microspheres using Modified Polymer Resin

Porosity in polymer parts is often desired to improve mechanical properties. Individual pores must be small enough that bulk mechanical properties are retained but significant enough to reduce the density of the material. Filler materials can be incorporated into polymer matrices and subsequently removed to create voids. The materials used to create the voids are known as pore-formers. The present research aims to create spherical pores in a silicone matrix by inserting and removing core materials or fillers post-cure. A method was developed to incorporate pore formers into an uncured polymer resin and remove the materials from the matrix. Polyethylene Glycol (PEG) and Polylactic Acid (PLA) microspheres are created and incorporated into silicone matrices as pore formers. Microspheres with controllable size distributions are formed via ultrasonic spray pyrolysis and emulsion formation. Microspheres are removed from the matrix by solvent extraction and calcination. PLA microspheres were modified by hydroxyl addition to the surface to study their solubility in water. PEG-PLA block copolymers are also synthesized and investigated, comparing their physical and chemical properties to the monomers to identify whether the block copolymer microspheres will be more easily removable than their monomeric microspheres. Moreover, other properties including thermal stability, rheology, and mechanical response are studied. The present dissertation provides a comprehensive understanding of the synthesis and characterization of PEG and PLA-based pore formers, toward the future development of feedstock for additive manufacturing porous structures.

Damptey, Ransford↗

Developing a Carbon Negative Biorefinery for Organic Waste Valorization

Production of bio-based chemicals have become increasingly attractive as efforts to meet carbon neutrality goals expand. Diverse organic waste feedstocks can be valorized via arrested anaerobic digestion and chain elongation to produce important key intermediates, such as medium chain carboxylic acids. Our work aims to develop a carbon negative biorefinery that funnels multiple organic waste feedstocks into a chemically consistent stream of carboxylic acids that are then upgraded to exemplary carbon negative products. The pairing of a hydrolysis reactor with a chain elongation reactor will allow each biological step to be optimized to improve the ability to valorize a variety of organic waste streams. Specifically, this work has so far been aimed at screening for potential chain elongating organisms to produce VFAs and MCCAs of interest. Four chain elongating organisms were tested for their chain elongation potential with diverse single and mixed substrates. So far, Megasphaera elsdenii and Actinobacillus succinogenes have been tested to determine potential differences in titer as well as product speciation due to variations in pH. To do this, each organism was tested under 3 different substrate combinations with pH maintained at either 5.5, 6, or 7. With better understanding of their metabolic needs and optimal operating conditions, these chain elongating organisms could provide a valuable option to facilitate the chain elongation necessary to produce precursor molecules. In addition to optimizing the bioconversion steps, downstream processing of carboxylic acids is also a key component for the overall feasibility of the process. Our group previously developed a downstream in-situ product recovery (ISPR) process for continuously recovering bio-based carboxylic acids from fermentation broth. The ISPR includes: (i) a solid-liquid separation as a cell retention device, (ii) a liquid-liquid extraction (LLE) to selectively extract the desired bio-based acids, and (iii) a distillation to obtain the neat product. The integrated process was demonstrated at bench-scale and is now scaled up for pilot-scale operations. A more cost-efficient membrane-based emulsion separation is introduced for LLE in downstream separation process with greatly promoted mass transfer, leading to -2800 times smaller needed membrane area than membrane contactors to achieve the same butyric acid extraction rate.

BIOMASS FUELS↗

Investigation of porous polydimethylsiloxane structures with tunable properties induced by the phase separation technique

This article reports the fabrication and characterization of porous polydimethylsiloxane (PDMS) structures developed by the solvent evaporationinduced phase separation technique. Here, ternary systems containing water/ tetrahydrofuran (THF)/PDMS with various concentrations are produced to form a stable solution. The porous PDMS structures are formed by removing the solvent (THF) and nonsolvent (water) phases during the stepping heat treatment procedure. The analytical ternary phase diagram is constructed based on the thermodynamic equilibrium state in the polymer solution to explain the stable/unstable formulations and the possible composition change path. The results show that the isolated pores with the adjustable pore size ranging from 330 to 1900 μm are obtained by tuning the water to the THF ratio. The mechanical properties of the porous PDMS structures are determined by conducting the tensile tests on the prepared dog bone-shaped specimens. A wide range of elastic modulus ranging between 0.49 and 1.05 MPa was achieved without affecting the density of the porous sample by adjusting the solvent and non-solvent content in the solution. It is shown that the flexibility of the porous structures can be improved by reducing the ratio of water to THF and decreasing the PDMS content. The porosity measurements reveal that the PDMS concentration is the major phase controlling the porosity of the structure, while the effect of water/THF is negligible.

42 ENGINEERING↗