Impact of WIN site inhibitor on the WDR5 interactome
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Guarnaccia, Alissa D.↗
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Results for “ROSES”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Isolation and characterization of cross-neutralizing coronavirus antibodies from COVID-19+ subjects
SARS-CoV-2 is one of three coronaviruses that have crossed the animal-to-human barrier and caused widespread disease in the past two decades. The development of a universal human coronavirus vaccine could prevent future pandemics. We characterize 198 antibodies isolated from four COVID-19+ subjects and identify 14 SARS-CoV-2 neutralizing antibodies. One targets the N-terminal domain (NTD), one recognizes an epitope in S2, and 11 bind the receptor-binding domain (RBD). Three anti-RBD neutralizing antibodies cross-neutralize SARS-CoV-1 by effectively blocking binding of both the SARS-CoV-1 and SARS-CoV-2 RBDs to the ACE2 receptor. Using the K18-hACE transgenic mouse model, we demonstrate that the neutralization potency and antibody epitope specificity regulates the in vivo protective potential of anti-SARS-CoV-2 antibodies. All four cross-neutralizing antibodies neutralize the B.1.351 mutant strain. Thus, our study reveals that epitopes in S2 can serve as blueprints for the design of immunogens capable of eliciting cross-neutralizing coronavirus antibodies.
60 APPLIED LIFE SCIENCES↗
Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies
Recognition of N-linked glycan at residue N276 (glycan276) at the periphery of the CD4-binding site (CD4bs) on the HIV-envelope trimer is a formidable challenge for many CD4bs-directed antibodies. To understand how this glycan can be recognized, here we isolate two lineages of glycan276-dependent CD4bs antibodies. Antibody CH540-VRC40.01 (named for donor-lineage.clone) neutralizes 81% of a panel of 208 diverse strains, while antibody CH314-VRC33.01 neutralizes 45%. Cryo-electron microscopy (cryo-EM) structures of these two antibodies and 179NC75, a previously identified glycan276-dependent CD4bs antibody, in complex with HIV-envelope trimer reveal substantially different modes of glycan276 recognition. Despite these differences, binding of glycan276-dependent antibodies maintains a glycan276 conformation similar to that observed in the absence of glycan276-binding antibodies. By contrast, glycan276-independent CD4bs antibodies, such as VRC01, displace glycan276 upon binding. These results provide a foundation for understanding antibody recognition of glycan276 and suggest its presence may be crucial for priming immunogens seeking to initiate broad CD4bs recognition.
59 BASIC BIOLOGICAL SCIENCES↗
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↗
VRC34-Antibody Lineage Development Reveals How a Required Rare Mutation Shapes the Maturation of a Broad HIV-Neutralizing Lineage
Rare mutations have been proposed to restrict the development of broadly neutralizing antibodies against HIV-1, but this has not been explicitly demonstrated. We hypothesized that such rare mutations might be identified by comparing broadly neutralizing and non-broadly neutralizing branches of an antibody-developmental tree. Because sequences of antibodies isolated from the fusion peptide (FP)-targeting VRC34-antibody lineage suggested it might be suitable for such rare mutation analysis, we carried out next-generation sequencing (NGS) on B cell transcripts from donor N123, the source of the VRC34 lineage, and functionally and structurally characterized inferred intermediates along broadly neutralizing and poorly neutralizing developmental branches. The broadly neutralizing VRC34.01 branch required the rare heavy-chain mutation Y33P to bind FP, whereas the early bifurcated VRC34.05 branch did not require this rare mutation and evolved less breadth. Our results demonstrate how a required rare mutation can restrict development and shape the maturation of a broad HIV-1-neutralizing antibody lineage.
59 BASIC BIOLOGICAL SCIENCES↗
Analyzing acoustic emission data to identify cracking modes in cement paste using an artificial neural network
This research is focused on the identification of cracking mechanisms for cement paste using acoustic emission data, recorded from compression and notched four-point bending tests. A procedure is developed for analyzing the data by employing an agglomerative hierarchical clustering method, an artificial neural network, and a ray-tracing source location algorithm. An agglomerative hierarchical clustering method is utilized to cluster the AE data from a compression test using frequency-dependent features. A neural network is trained using the compression test data and applied to the AE data emitted during the four-point bending test. The clustered data from the four-point bending test is localized using a ray-tracing algorithm. Based on the occurrence and locations of the clustered events and signal feature analyses, potential cracking mechanisms are identified and assigned.
36 MATERIALS SCIENCE↗
Genarris 2.0: A Random Structure Generator for Molecular Crystals
Genarris is an open source Python package for generating random molecular crystal structures with physical constraints for seeding crystal structure prediction algorithms and training machine learning models. Here we present a new version of the code, containing several major improvements. A MPI-based parallelization scheme has been implemented, which facilitates the seamless sequential execution of user-defined workflows. A new method for estimating the unit cell volume based on the single molecule structure has been developed using a machine-learned model trained on experimental structures. A new algorithm has been implemented for generating crystal structures with molecules occupying special Wyckoff positions. A new hierarchical structure check procedure has been developed to detect unphysical close contacts efficiently and accurately. New intermolecular distance settings have been implemented for strong hydrogen bonds. To demonstrate these new features, we study two specific cases: benzene and glycine. Genarris finds the experimental structures of the two polymorphs of benzene and the three polymorphs of glycine. Program summary Program Title: Genarris 2.0 Program Files doi: http://dx.doi.org/10.17632/grx6mz4pjn.1 Licensing provisions: BSD-3 Clause Programming language: Python, C External routines/libraries: Spglib, ASE, pymatgen, SciPy, mpi4py, scikit-learn, PyTorch, FHI-aims. Nature of problem: Molecular crystal structure prediction. Solution method: Genarris 2.0 generates molecular crystal structures over the 230 space groups, on general and special Wyckoff positions, using physical constraints. Down-sampling of the generated structures may be performed subsequently, based on molecular crystal packing descriptors and an unsupervised machine learning algorithm. Lastly, ab initio structure relaxation may be performed for the final pool. Depending on the user-defined workflow implemented, Genarris may be used to generate diverse molecular crystal datasets to seed evolutionary algorithms or to train machine learning algorithms or as a standalone crystal structure prediction method. Restrictions: For crystal structure generation, the molecule of interest must be semi-rigid with no bond rotational degrees of freedom. Unusual features: Genarris 2.0 is a highly distributed program, making use of MPI for Python parallelization. The user has the ability to design and implement workflows by executing a user-defined list of procedures. Genarris 2.0 offers new features including a machine learning model for estimating the molecular volume in the solid state from the single molecule structure, structure generation in special Wyckoff positions of space groups, hierarchical structure checks including rigorous treatment of non-orthogonal structures, and clustering and down-selection workflows combining first principles simulations with machine learning. (C) 2020 Elsevier B.V. All rights reserved.
Crystal structure prediction↗
Implicit highly-coupled single-ion Hall-MHD formulation for hybrid particle-in-cell codes
The rudiments of a particle-based single-fluid two-temperature magnetohydrodynamic (MHD) algorithm have been outlined in Thoma et al. (2013). The extension of this algorithm to include the effect of Hall physics is described in this paper. An implicit leapfrog version of the algorithm, which allows timesteps large compared to the resistive decay time and other relevant timescales, has recently been added to a hybrid particle-in-cell code. In standard MHD the Hall term in the generalized Ohm’s law can often be neglected when the Hall parameter is small. This term must, however, be retained in regimes where it is non-negligible. The retention of displacement current in Maxwell’s equations avoids the numerical difficulties associated with the whistler mode, which are encountered in standard explicit Hall-MHD codes, and allows the algorithm to be incorporated into hybrid particle-in-cell codes, for which particles may migrate from a kinetic to fluid to MHD description based upon local ambient plasma conditions. A highly-coupled implicit Hall-MHD formalism is presented, in which displacement current can either be retained or neglected. Even when displacement current is neglected, the highly-coupled implicit formalism avoids the restrictive timesteps for the whistler mode in explicit Hall-MHD codes. A comparison of numerical and analytic dispersion analysis demonstrates the feasibility of this approach and establishes relevant constraints to assure numerical stability. The implementation of the algorithm is described, and test simulation results in 1D and 2D in both linear and nonlinear regimes are presented.
97 MATHEMATICS AND COMPUTING↗
A database and framework for carbon ore resources and associated supply chain data
Not Available
Justman, Devin↗
A curated data resource to support safe carbon dioxide transport-route planning
Not Available
29 ENERGY PLANNING, POLICY, AND ECONOMY↗
Interactive effects of microbial functional diversity and carbon availability on decomposition – A theoretical exploration
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
Scaling of energy delivered through an electrostatic discharge to a small series load
We study the energy delivered through a small-resistance series “victim” load during electrostatic discharge events in air. For gap lengths over 1 mm, the fraction of the stored energy delivered is mostly gap-length independent, with a slight decrease at larger gaps due to electrode geometry. The energy to the victim scales linearly with circuit capacitance and victim load resistance but is not strongly dependent on circuit inductance. This scaling leads to a simple approach to predicting the maximum energy that will be delivered to a series resistance for the case where the victim load resistance is lower than the spark resistance.
42 ENGINEERING↗
Daylight simulation workflows incorporating measured bidirectional scattering distribution functions
Daylight predictions of architectural spaces depend on good estimates of light transfer through skylights, windows and other fenestration systems. For clear glazing and painted surfaces, parametric transmission and reflection models have proven adequate, but there are many cases where light-scattering, semi-specular shading and daylighting materials defy simple characterization. Something as commonplace as fabric roller shades and venetian blinds may turn daylight prediction into guesswork, and numerous advanced systems on the market tuned specifically to enhance daylight are not sufficiently characterized to distinguish their performance. In this paper, we describe new tools available to handle novel and specialized fabrics, materials, and devices using data-driven modelling of bi-directional scattering distribution functions (BSDFs). These representations are usually tabulated at constant or adjustable angular resolution for efficient point-in-time and annual daylight simulations. We describe a variety of BSDF simulation workflows, including some of the tools and methods that make advanced analysis possible, and highlight some of the current challenges. We conclude with a discussion of future work and how such data might be created and shared worldwide.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
Component-based SHGC determination of BIPV glazing for product comparison
Building-integrated photovoltaic (BIPV) systems are intrinsically designed to generate electricity and to provide at least one building-related function. When BIPV modules act as glazing products in windows, skylights or curtain walls, their ability to control the transmission of solar energy into the building must be characterised by a Solar Heat Gain Coefficient (SHGC) or g value (also known as Total Solar Energy Transmittance – TSET – or “solar factor”). For the comparison of BIPV glazing products consisting of one PV laminate and possibly further, conventional glazing layers separated by gas-filled cavities, the procedures documented in international standards for architectural glazing (e.g. ISO 9050 and EN 410) form a suitable starting point. Easily implemented modifications to these procedures are proposed to take both optical inhomogeneity (if relevant) and extraction of electricity from BIPV glazing units into account. Geometrically complex glazing and shading devices, and light-scattering glazing layers, are outside the scope of the proposed methodology; SHGC determination for obliquely incident solar radiation is also excluded. For these cases, the experimental calorimetric approach documented in [ISO 19467:2017; ISO 19467-2:2021] is recommended. The paper also presents results and conclusions from an implementation exercise and sensitivity study carried out by participants of the IEA-PVPS Task 15 on BIPV. The cell coverage ratio in the PV laminate, the thermal resistance offered by the glazing configuration, the choice of boundary conditions and the effect of extracting electricity were all identified as parameters which significantly affect the SHGC value determined for a given type of BIPV glazing. A practicable approach to accommodate the great variety of dimensions typical for BIPV glazing is also proposed. These findings should pave the way for modifying the existing component-based standards for architectural glazing to take the specific features of BIPV glazing into account.
14 SOLAR ENERGY↗
Perspectives on the relationship between materials chemistry and roll-to-roll electrode manufacturing for high-energy lithium-ion batteries
As lithium-ion battery (LIB) active material and cell manufacturing costs continue to drop with wider adoption of electric vehicles, electrode and cell processing costs remain too high in terms of reaching the ultimate U.S. Department of Energy (DOE) cell cost target of $80/kWh. This paper primarily covers major materials chemistry advancements made over the last 10 years at Oak Ridge National Laboratory (ORNL) in the space of advanced manufacturing science for LIBs with the aim of simultaneously meeting the ultimate cost target, 500 Wh/kg gravimetric energy density, 10-15-min fast charge times, and 1000 deep discharge cycles. Aqeous electrode processing with a variety of active anode and cathode materials is now a standard procedure at the DOE Battery Manufacturing R&D Facility at ORNL (BMF), including the latest processes developed for Ni-rich cathodes. New results on cobalt-free LiNi 0.8 Fe 0.1 Al 0.1 O 2 (NFA 811) are also included and discussed in an electrode processing advantage context. In addition, colloidal processing advancements have been made for Si/C composite anodes for achieving >600 mA h/g capacities. Optimization of electrode coating parameters and drying protocols have been completed, which has elucidated how key processing variables need to be changed when parameters such as slurry solids loading, solvent type, and wet electrode thickness are changed. ORNL has also increased the line speeds at which thick cathodes can be processed using ultra-fast electron beam (EB) curing and substantially decreased formation cycling times to <1 day. Finally, key details of these advancements are discussed in the context of materials chemistry and process-property-performance relationships.
25 ENERGY STORAGE↗
Achieving low-temperature hydrothermal relithiation by redox mediation for direct recycling of spent lithium-ion battery cathodes
Lithium-ion battery (LIB) recycling is an urgent need to address the massive generation of spent LIBs from portable devices and electrical vehicles. However, the large-scale recycling is hampered by economic and safety issues associated with today's recycling processes. In this study, we demonstrate a safe and energy efficient direct regeneration process based on low-temperature hydrothermal relithiation (LTHR) at low pressure for spent LiNi x Co y Mn z O 2 (0 < x,y,z <1, x + y + z = 1, or NCM) cathode materials. A low concentration of low-cost redox mediator is employed to improve the relithiation kinetics of spent NCM materials, enabling full relithiation temperature to be reduced from 220 °C to 100 °C or below. Correspondingly, the pressure incurred in the relithiation process can be reduced from ~25 bar to 1 bar, offering significantly improved operation safety. Specifically, three NCM materials, including chemically delithiated NCM111, cycled (degraded) NCM111, and cycled NCM622, were successfully regenerated with complete recovery of composition, crystal structure, and electrochemical performance, achieving the same effectiveness as that achieved at high temperature process. Meanwhile, the total energy consumption of spent cell recycling and the greenhouse gas emission is also reduced. This work provides a facile and scalable way to more sustainable LIB recycling with high economic return, high operation safety and low cost.
25 ENERGY STORAGE↗