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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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At least 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Hidden first-order phase transitions and large magnetocaloric effects in GdNi 1-x Co x

We report a large magnetocaloric effect tunable between 70 and 115 K in a series of rare earth intermetallic compounds GdNi 1-x Co x with x varying from 0 to 0.15 that manifest rather unconventional second-order phase transitions with concurrent changes in both magnetic and crystallographic sublattices. While the Curie temperature, TC, linearly increases with x(Co), the maximum isothermal entropy change induced by magnetic field varying between 0 and 50 kOe slightly decreases from 14 J/kg K at 71 K when x(Co) = 0 to10 J/kg K at 115 K when x(Co) = 0.15. Additionally, the temperature-averaged entropy change figures of merit calculated at temperature spans of 10 K for all examined compositions are comparable to those of the best known magnetocaloric materials that exhibit second-order phase transitions, including elemental Gd and La(Fe,Co,Si) 13 alloys. Through a detailed analysis of the magnetic field-induced entropy changes along with assessment of critical exponents we explore the role magneto-elastic coupling plays in controlling magnetocaloric properties of GdNi 1-x Co x compounds. We also formulate a model based on the mean field theory approximation to describe both magnetic and magnetocaloric properties of the title materials in qualitative agreement with experimental results.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Determination of the mutual orientation between proton CSA tensors mediated through band-selective 1 H– 1 H recoupling under fast MAS

We report the mutual orientation of nuclear spin interaction tensors provides critical information on the conformation and arrangement of molecules in chemicals, materials, and biological systems at an atomic level. Proton is a ubiquitous and important element in a variety of substances, and its NMR is highly sensitive due to their virtually 100% natural abundance and large gyromagnetic ratio. Nevertheless, the measurement of mutual orientation between the 1 H CSA tensors has remained largely untouched in the past due to strong 1 H– 1 H homonuclear interactions in a dense network of protons. In this study, we have developed a proton-detected 3D 1 H CSA/ 1 H CSA/ 1 H CS correlation method that utilizes three techniques to manage homonuclear interactions, namely fast magic-angle spinning, windowless C-symmetry-based CSA recoupling (windowless-ROCSA), and a band-selective 1 H– 1 H polarization transfer. The asymmetric 1 H CSA/ 1 H CSA correlated powder patterns produced by the C-symmetry-based methods are highly sensitive to the sign and asymmetry parameter of the 1 H CSA, and the Euler angle β as compared to the symmetric pattern obtained by the existing γ-encoded R-symmetry-based CSA/CSA correlation methods and allows a larger spectral area for data fitting. These features are beneficial for determining the mutual orientation between the nuclear spin interaction tensors with improved accuracy.

1H CSA↗
DOE OSTI2021

In Silico Discovery of Multistep Chemistry Initiated by a Conical Intersection: The Challenging Case of Donor–Acceptor Stenhouse Adducts

Detailed mechanistic understanding of multistep chemical reactions triggered by internal conversion via a conical intersection is a challenging task that emphasizes limitations in theoretical and experimental techniques. We present a discovery-based, hypothesis-free computational approach based on first-principles molecular dynamics to discover and refine the switching mechanism of donor–acceptor Stenhouse adducts (DASAs). We simulate the photochemical experiment in silico, following the “hot” ground state dynamics for 10 ps after photoexcitation. Using state-of-the-art graphical processing units-enabled electronic structure calculations we performed in total ~2 ns of nonadiabatic ab initio molecular dynamics discovering (a) critical intermediates that are involved in the open-to-closed transformation, (b) several competing pathways which lower the overall switching yield, and (c) key elements for future design strategies. Finally, our dynamics describe the natural evolution of both the nuclear and electronic degrees of freedom that govern the interconversion between DASA ground-state intermediates, exposing significant elements for future design strategies of molecular switches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Isolated copper–tin atomic interfaces tuning electrocatalytic CO 2 conversion

Direct experimental observations of the interface structure can provide vital insights into heterogeneous catalysis. Examples of interface design based on single atom and surface science are, however, extremely rare. Here, we report Cu–Sn single-atom surface alloys, where isolated Sn sites with high surface densities (up to 8%) are anchored on the Cu host, for efficient electrocatalytic CO 2 reduction. The unique geometric and electronic structure of the Cu–Sn surface alloys (Cu 97 Sn 3 and Cu 99 Sn 1 ) enables distinct catalytic selectivity from pure Cu 100 and Cu 70 Sn 30 bulk alloy. The Cu 97 Sn 3 catalyst achieves a CO Faradaic efficiency of 98% at a tiny overpotential of 30 mV in an alkaline flow cell, where a high CO current density of 100 mA cm –2 is obtained at an overpotential of 340 mV. Density functional theory simulation reveals that it is not only the elemental composition that dictates the electrocatalytic reactivity of Cu–Sn alloys; the local coordination environment of atomically dispersed, isolated Cu–Sn bonding plays the most critical role.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Exploring the impact of Cr-doping on the crystallographic and magnetic structure of Mn 5 Si 3 antiferromagnetic alloy

Here, the role of Cr-doping on the structural and magnetic ground states of Mn 5 Si 3 alloy has been investigated through temperature-dependent neutron powder diffraction (NPD) and X-ray absorption fine structure (XAFS) techniques. All the Cr-doped alloys of nominal composition Mn 5-x Cr x Si 3 (for x = 0.05, 0.1, and 0.2) undergo two first-order magneto-structural phase transitions from hexagonal (space group: P6 3 /mcm) paramagnetic → orthorhombic (space group: Ccmm) collinear antiferromagnetic → orthorhombic (space group: Cc2m) non-collinear antiferromagnetic phase on cooling from room temperature. NPD studies at different constant temperatures indicate that both anti ferromagnetic phases are commensurate in nature and can be represented by q = (0,1,0) magnetic propagation vector for all the Cr-doped alloys. Such doping at the Mn-site results in a significant modification of the non-collinear antiferromagnetic structure (both moment size and orientation) and hence affects the unusual magnetic properties, like inverted hysteresis loop, thermomagnetic irreversibility, etc. The XAFS measurements were performed to interpret the local environment of doped Cr atoms in detail, which is critical for a microscopic understanding of the unusual properties of this class of Cr-doped Mn 5 Si 3 alloys. The analysis confirms the elemental state of Cr in the doped alloys and indicates a high degree of preservation of local crystallographic structure with varying Cr concentration and sample temperature. Doping induces intriguing changes in XAFS patterns, elucidated through different types of scattering mechanisms associated with the central absorbing Cr atom.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Yttrium Hydride Post Irradiation Examination Plan

The overarching goal of the Department of Energy Office of Nuclear Energy (DOE-NE) microreactor program is to develop technologies for the deployment of civilian microreactors by stakeholders1. Microreactors are expressed as advanced transportable nuclear reactors operating at low power (<20MWth) but high temperatures (>600°C), as well as plug-and-play and inherently safe designs. One prerequisite of a microreactor is the compactness, so that a truck can transport the reactor under safe conditions with the current road infrastructure1,2. The compactness of these reactors likely can be attainable by use of solid components for the essentials of the nuclear core, such as fuel, core heat removal components, reflectors, and moderators. Among these essentials, where fuel enrichment must remain < 20% to meet High Assay Low Enrichment Uranium criteria (HALEU), the largest contribution to the compactness is offered by use of solid moderators which benefit from light atomic weight elements, such as hydrogen, carbon, and beryllium2. Among these, hydrogen-bearing materials, such as metal hydrides, are superior to other options from the lowest critical mass standpoint. Noting that, factors other than critical mass should be considered for a specific reactor design. Yttrium- or zirconium-based metal hydrides have been down-selected due to their neutronic performance. In addition to the neutronic perspective, maintaining hydrogen within the metal hydride is important at the high operating temperatures proposed by advanced reactors. Yttrium hydride (YHx) is, therefore, a proposed moderator material that offers better hydrogen retention at higher operating temperatures than zirconium hydrides due to higher retention and thermal stability of hydrogen in the metal3. The irradiated materials properties of metal hydrides, in this case YHx, must be assessed for the qualification of these moderators. Material testing and inspection processes must illustrate that the effects of dimensional and property changes on thermophysical and mechanical properties do not cause any significant changes on the microreactor safety, and the moderating power is maintained within design limits. Thus, the effect of irradiation on the thermophysical and mechanical properties must be determined. This post-irradiation examination (PIE) plan specifically aims to determine these properties for YHx following Advanced Test Reactor (ATR) irradiation.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2025

Rapid T cell engineering to counter emerging threats

There is a critical need for new approaches to effectively counter emerging pathogens, especially those which do not respond to antibodies or antibiotics. T cells represent an essential element of native immune response in many of the deadliest pathogens: controlling T cell reactivity and behavior would allow for countermeasures for currently untreatable diseases from cancer to coronaviruses, especially if using a patient’s own T cells (autologous) where no host rejection will occur. However, current methods for modifying T cells, e.g., FDA-approved chimeric antigen receptor T cell (CAR) approaches, require genetic manipulation and expansion which can take weeks to generate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Success Path Method: Introduction to the Success Path Method Software Tool©

As part of its commitment to advancing safety and reliability assessment methodologies, Argonne National Laboratory pioneered the use of an evaluation method called the Success Path Method (SPM) to improve risk management for offshore oil and gas operations. The development of the SPM at Argonne has been driven by the need to improve existing risk assessment methodologies by focusing on the steps necessary for success rather than failure modes alone. This is particularly important for industrial environments like offshore facilities that perform multiple functions under a continuously evolving set of operational conditions – such as water depth and temperature, currents, and weather conditions. In these dynamic environments, the traditional Probabilistic Risk Assessment (PRA) approach is far too complex as it focuses on what can go wrong – which comprises an infinite failure space that must be fully explored and understood. By shifting the focus to a finite space of success paths, the SPM enables operators and decision makers to prioritize a manageable number of steps that must go right to ensure success. Building on its five decades of experience in safety assessments for the nuclear industry, Argonne made major adaptations to existing risk assessment methods utilizing features similar to fault trees that are traditionally used in PRA to map all pathways in which the system can malfunction. In contrast, SPM identifies the components and processes that must function correctly to achieve specific outcomes – such as preventing the uncontrolled release of hydrocarbons during drilling operations. The SPM framework integrates equipment, procedures, software, processes, and human actions to ensure that physical barriers meet critical safety functions in dynamic operational conditions. This approach helps identify failure modes and improve operational risk management by narrowing the focus to key success elements, which in turn reduces uncertainty and helps users understand, manage, and respond to failures.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Structural Aspects of Neutron Survival Probabilities

The neutron survival probability (and related quantities including probabilities of extinction and initiation) is a central element of the broader stochastic theory of neutron populations and finds application in fields including reactor start-up, analysis of reactor power bursts and criticality accidents, and safeguards. In a full neutron transport formulation, the equation governing the single-neutron survival probability is a backward or adjoint-like integro-partial differential equation with the added complexity of being highly nonlinear. Analogous formulations of this equation exist in the context of many approximate theories of neutron transport, with the point kinetics formulation having received significant theoretical attention since the 1940s. This work continues this tradition by providing a novel analysis of the single-neutron survival probability equation using the tools of boundary layer theory. The analysis reveals that the “fully dynamic” solution of the single-neutron survival probability equation—and some key probability distributions derived from it—may be cast as a singular perturbation around the underlying quasi-static single-neutron probability of initiation. In this perturbation solution, the expansion parameter is the ratio of the neutron generation time to a macroscopic time scale characterizing the overall system evolution; this interpretation illuminates some of the fundamental structural aspects of neutron survival phenomena.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

PLN-6268 Yttrium Hydride Post Irradiation Examination Plan

The overarching goal of the Department of Energy Office of Nuclear Energy (DOE-NE) microreactor program is to develop technologies for the deployment of civilian microreactors by stakeholders1. Microreactors are expressed as advanced transportable nuclear reactors operating at low power (<20MWth) but high temperatures (>600°C), as well as plug-and-play and inherently safe designs. One prerequisite of a microreactor is the compactness, so that a truck can transport the reactor under safe conditions with the current road infrastructure1,2. The compactness of these reactors likely can be attainable by use of solid components for the essentials of the nuclear core, such as fuel, core heat removal components, reflectors, and moderators. Among these essentials, where fuel enrichment must remain < 20% to meet High Assay Low Enrichment Uranium criteria (HALEU), the largest contribution to the compactness is offered by use of solid moderators which benefit from light atomic weight elements, such as hydrogen, carbon, and beryllium2. Among these, hydrogen-bearing materials, such as metal hydrides, are superior to other options from the lowest critical mass standpoint. Noting that, factors other than critical mass should be considered for a specific reactor design. Yttrium- or zirconium-based metal hydrides have been down-selected due to their neutronic performance. In addition to the neutronic perspective, maintaining hydrogen within the metal hydride is important at the high operating temperatures proposed by advanced reactors. Yttrium hydride (YHx) is, therefore, a proposed moderator material that offers better hydrogen retention at higher operating temperatures than zirconium hydrides due to higher retention and thermal stability of hydrogen in the metal3. The irradiated materials properties of metal hydrides, in this case YHx, must be assessed for the qualification of these moderators. Material testing and inspection processes must illustrate that the effects of dimensional and property changes on thermophysical and mechanical properties do not cause any significant changes on the microreactor safety, and the moderating power is maintained within design limits. Thus, the effect of irradiation on the thermophysical and mechanical properties must be determined. This post-irradiation examination (PIE) plan specifically aims to determine these properties for YHx following Advanced Test Reactor (ATR) irradiation.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2025

NdPO 4 solubility and aqueous Neodymium speciation in supercritical fluids: An experimental study at 500–700 °C and 1.7 kbar

A key aspect in the formation of rare earth elements (REE) deposits is the role of REE transport as aqueous REE complexes in supercritical hydrothermal solutions, where the nature of the aqueous complex is controlled by solution composition, temperature and pressure. Despite chloride being considered as one of the most abundant transporting ligands in magmatic-hydrothermal fluids, experimental investigations on the stability of aqueous REE chloride complexes are scarce above 300 °C. In this study, synthetic NdPO 4 crystals were reacted with non-saline and saline (0, 0.05 and 0.5 mNaCl), acidic (0.01 mHCl) aqueous solutions in a series of solubility experiments conducted at 500–700 °C and 1.7 kbar, where the solubilities were determined using a stable Nd isotope ( 145 Nd isotope spike) dilution technique. NdPO 4 solubility ranges between 28 ppm and 10,858 ppm, where solubility increases with both temperature and salinity. At 500 °C, log mNdPO 4 increases from –3.93 to –1.60 and there is a strong correlation between NdPO 4 solubility and NaCl concentrations (slope of 1.2 ± 0.3), indicating stabilization of the Nd chloride aqueous complexes with a stoichiometry corresponding to NdCl 2+ . At 600 °C, this correlation is weaker (slope of 0.4, log mNdPO 4 increases from –2.63 to –1.88) indicating the stabilization of both Nd chloride and hydroxyl species controlling solubility. At 700 °C, NdPO 4 solubility is largely independent of NaCl concentration indicating that solubility is controlled by Nd hydroxyl complexes, where stoichiometry suggests the neutral Nd(OH) 3 0 species is dominant. The solubility product (Ksp) of NdPO4 is derived from experimental data with the relation: log K sp = -41.81 – 0.057T – 20987/T, with T temperature in Kelvin. Comparison of the measured Nd phosphate solubility to thermodynamic predictions using the available Helgeson-Kirkham-Flowers equation of state parameters for aqueous Nd complexes indicate that predictions are up to three orders of magnitude lower compared to experimental observations. This discrepancy is most pronounced in saline solutions, suggesting that thermodynamic properties of the REE chloride species in supercritical fluids require revision. Numerical simulations of fluid-rock interaction between acidic, saline fluids and a Strange Lake felsic mineral assemblage demonstrates that NdPO 4 solubility predictions from models are four to six orders of magnitude lower than those calculated based on empirical fits from experiments, which suggests that acidic, saline fluids may play an important role in mobilizing large amounts of light REE from 450 to 700 °C.

58 GEOSCIENCES↗
DOE OSTI2026

Numerical Investigation of Fluid Flow and Space Charge in Liquid Argon Time Projection Chamber (LArTPC) Detectors

Overview This project focused on developing a high-fidelity numerical framework to simulate the multiphysics environment within Liquid Argon Time Projection Chamber (LArTPC) detectors. The primary objective was to characterize the complex interplay between ion transport, background fluid dynamics, and electric field distortions—a critical factor for the calibration and sensitivity of next-generation High Energy Physics experiments, such as DUNE. Technical Achievements The research successfully yielded a hybrid numerical space-charge solver utilizing a Cell-Centered Finite Volume Method (FVM) for ion transport coupled with a Finite Element Method (FEM) for electric potential. Key accomplishments include: • Verification & Validation: The 3-D solver was rigorously verified against 1-D analytical solutions, demonstrating high numerical accuracy in predicting space-charge-induced field deviations. • Field Distortion Analysis: 3D simulations revealed that space charge effects introduce significant non-uniformities in the electric field. Critically, the research identified that background LAr flow velocities, when comparable to ion drift velocities, markedly exacerbate these distortions. • Technology Transfer: The resulting source code and comprehensive user manuals were successfully transferred to collaborators at Fermilab, providing a portable computational tool for the broader scientific community. Challenges and Future Directions While the space-charge solver achieved all performance metrics, the integrated fluid dynamics modeling encountered convergence challenges stemming from the extreme 200-fold disparity in length scales between the detector's 37 mm inlet pipes and the 8-meter global domain. To address this, the project has identified a clear technical pivot toward Hierarchical Geometric Adaptive Mesh Refinement (HG-AMR). By implementing an h-type refinement strategy with hanging nodes, future iterations of this solver will be capable of resolving localized high-gradient inlet flows without the prohibitive computational costs of regular grids. This advancement, combined with data-driven uncertainty quantification based on MicroBooNE-style calibration, will enable the precise modeling of detector responses in large-scale cryogenic environments where direct measurement remains difficult. Impact The computational tools developed under this award provide a foundation for enhancing the energy resolution and spatial reconstruction of noble liquid detectors. By bridging the gap between theoretical fluid dynamics and experimental field calibration, this work supports the DOE’s mission to advance the frontiers of neutrino physics and dark matter detection.

42 ENGINEERING↗
DOE OSTI2024

Core Characterization: Computer Tomography, Geochemical, and Core Petrophysical Workflows for Emerging Critical Mineral Plays

The National Energy Technology Laboratory’s geoimaging lab in Morgantown, WV has been performing core characterization using multi-resolution Computed Tomography (CT) imaging and multisensor corelogger which allows for cm-resolution elemental and petrophysical measurements along whole core. This workflow has historically been used in unconventional gas plays and potential carbon storage locations. This rapid core characterization leads itself well as a first phase process in CM/REE evaluation efforts allowing for high-resolution, non-destructive investigation of elemental concentration using X-Ray Fluorescence and examination of core features through CT imaging.

Paronish, Thomas J.↗
DOE OSTI2024

Component Criticality in BESS for Cybersecurity

Battery energy storage systems (BESS), inverters, and associated digital equipment are integral pieces of interdependent energy delivery systems. When considering the supply chain security of such systems, there is often a misplaced focus on the origin of energy generation and storage materials like battery cells, overlooking the more significant cyber risks that stem from digital power electronics control systems. Part of this misplaced focus is due to the relative costs of these components, with more attention given to expensive raw materials rather than the impactful digital elements themselves. The Idaho National Laboratory (INL) is addressing this gap in supply chain security through a systems-of-systems approach that considers the impact various components in digital energy systems can have should misoperation occur. Therefore, INL assigns a cyber criticality score based on quantitative analysis, which enables informed prioritization of mitigations and allows operators to reduce risk in light of the prevalence of a BESS and associated systems foreign supply chain.

25 ENERGY STORAGE↗
DOE OSTI2025

A novel peridynamics-based approach to predict pharmaceutical tablet robustness

The pharmaceutical drug product development process can be greatly accelerated through the use of modeling and simulation techniques to predict the manufacturability and performance of a given formulation. The anticipation and possible mitigation of tablet damage due to manufacturing stresses represents a specific area of interest in the pharmaceutical industry for predicting formulation and tableting performance. While the finite element method (FEM) has been extensively used for predicting the mechanical behavior of powder material in the compaction processes, a shortcoming of the approach is the inherent difficulty to predict discontinuities (e.g., damage or cracking) within a tablet as FEM is a continuum-based approach. In this work, we propose a novel method utilizing peridynamics (PD), a numerical method that can capture discontinuities such as tablet fracture, to predict the evolution of damage and breakage in pharmaceutical tablets. The approach links (1) the finite element method – to elucidate the behavior of powders during die compaction – with (2) the peridynamics modeling technique – to model the discontinuous nature of damage and predict tablet breakage during the critical stages of unloading and ejection from the compression die. This short communication presents a proof of concept including a workflow to calibrate the linked FEM-PD simulation models. Further, it demonstrates promising results from a preliminary experimental validation of the approach. Following further development, this approach could be used to guide the optimization of compression processes through targeted changes to formulation material properties, compression process conditions, and/or tooling geometries to deliver improved process efficiency and tablet robustness.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Additive manufacturing of soft and hard magnetic materials used in electrical machines

Soft and hard magnetic materials were fabricated using additive manufacturing (AM) for use in 3D electrical machines. The effect of the characteristics and the nature of the magnetic feedstock powders was evaluated for both the cold spray (CS) and the fused filament fabrication (FFF) processes. 3D finite element analysis (FEA) was used to develop new motor topologies based on the advantages offered by AM. FEA optimization also allowed the identification of the most critical material properties and is thus a powerful tool to facilitate material development.

Bernier, Fabrice↗
DOE OSTI2021

StressNet - Deep learning to predict stress with fracture propagation in brittle materials

Abstract Catastrophic failure in brittle materials is often due to the rapid growth and coalescence of cracks aided by high internal stresses. Hence, accurate prediction of maximum internal stress is critical to predicting time to failure and improving the fracture resistance and reliability of materials. Existing high-fidelity methods, such as the Finite-Discrete Element Model (FDEM), are limited by their high computational cost. Therefore, to reduce computational cost while preserving accuracy, a deep learning model, StressNet, is proposed to predict the entire sequence of maximum internal stress based on fracture propagation and the initial stress data. More specifically, the Temporal Independent Convolutional Neural Network (TI-CNN) is designed to capture the spatial features of fractures like fracture path and spall regions, and the Bidirectional Long Short-term Memory (Bi-LSTM) Network is adapted to capture the temporal features. By fusing these features, the evolution in time of the maximum internal stress can be accurately predicted. Moreover, an adaptive loss function is designed by dynamically integrating the Mean Squared Error (MSE) and the Mean Absolute Percentage Error (MAPE), to reflect the fluctuations in maximum internal stress. After training, the proposed model is able to compute accurate multi-step predictions of maximum internal stress in approximately 20 seconds, as compared to the FDEM run time of 4 h, with an average MAPE of 2% relative to test data.

36 MATERIALS SCIENCE↗
DOE OSTI2020

CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data

Abstract CRISPR arrays and CRISPR-associated (Cas) proteins comprise a widespread adaptive immune system in bacteria and archaea. These systems function as a defense against exogenous parasitic mobile genetic elements that include bacteriophages, plasmids and foreign nucleic acids. With the continuous spread of antibiotic resistance, knowledge of pathogen susceptibility to bacteriophage therapy is becoming more critical. Additionally, gene-editing applications would benefit from the discovery of new cas genes with favorable properties. While next-generation sequencing has produced staggering quantities of data, transitioning from raw sequencing reads to the identification of CRISPR/Cas systems has remained challenging. This is especially true for metagenomic data, which has the highest potential for identifying novel cas genes. We report a comprehensive computational pipeline, CasCollect, for the targeted assembly and annotation of cas genes and CRISPR arrays—even isolated arrays—from raw sequencing reads. Benchmarking our targeted assembly pipeline demonstrates significantly improved timing by almost two orders of magnitude compared with conventional assembly and annotation, while retaining the ability to detect CRISPR arrays and cas genes. CasCollect is a highly versatile pipeline and can be used for targeted assembly of any specialty gene set, reconfigurable for user provided Hidden Markov Models and/or reference nucleotide sequences.

Podlevsky, Joshua D.↗