Search NASA⌕ Search

SEARCH · Search NASA

Results for “programmable”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,243 records · Page 69

chatHPC: Empowering HPC users with large language models

The ever-growing number of pre-trained large language models (LLMs) across scientific domains presents a challenge for application developers. While these models offer vast potential, fine-tuning them with custom data, aligning them for specific tasks, and evaluating their performance remain crucial steps for effective utilization. However, applying these techniques to models with tens of billions of parameters can take days or even weeks on modern workstations, making the cumulative cost of model comparison and evaluation a significant barrier to LLM-based application development. To address this challenge, we introduce an end-to-end pipeline specifically designed for building conversational and programmable AI agents on high performance computing (HPC) platforms. Our comprehensive pipeline encompasses: model pre-training, fine-tuning, web and API service deployment, along with crucial evaluations for lexical coherence, semantic accuracy, hallucination detection, and privacy considerations. Here, we demonstrate our pipeline through the development of chatHPC, a chatbot for HPC question answering and script generation. Leveraging our scalable pipeline, we achieve end-to-end LLM alignment in under an hour on the Frontier supercomputer. We propose a novel self-improved, self-instruction method for instruction set generation, investigate scaling and fine-tuning strategies, and conduct a systematic evaluation of model performance. The established practices within chatHPC will serve as a valuable guidance for future LLM-based application development on HPC platforms.

97 MATHEMATICS AND COMPUTING↗

Experimental Examination of Additively Manufactured Patterns on Structural Nuclear Materials for Digital Image Correlation Strain Measurements

Abstract Background There are a limited number of commercially available sensors for monitoring the deformation of materials in-situ during harsh environment applications, such as those found in the nuclear and aerospace industries. Such sensing devices, including weldable strain gauges, extensometers, and linear variable differential transformers, can be destructive to material surfaces being investigated and typically require relatively large surface areas to attach (> 10 mm in length). Digital image correlation (DIC) is a viable, non-contact alternative to in-situ strain deformation. However, it often requires implementing artificial patterns using splattering techniques, which are difficult to reproduce. Objective Additive manufacturing capabilities offer consistent patterns using programmable fabrication methods. Methods In this work, a variety of small-scale periodic patterns with different geometries were printed directly on structural nuclear materials (i.e., stainless steel and aluminum tensile specimens) using an aerosol jet printer (AJP). Unlike other additive manufacturing techniques, AJP offers the advantage of materials selection. DIC was used to track and correlate strain to alternative measurement methods during cyclic loading, and tensile tests (up to 1100 µɛ) at room temperature. Results The results confirmed AJP has better control of pattern parameters for small fields of view and facilitate the ability of DIC algorithms to adequately process patterns with periodicity. More specifically, the printed 100 μm spaced dot and 150 μm spaced line patterns provided accurate measurements with a maximum error of less than 2% and 4% on aluminum samples when compared to an extensometer and commercially available strain gauges. Conclusion Our results highlight a new pattern fabrication technique that is form factor friendly for digital image correlation in nuclear applications.

Novich, K. A. (ORCID:0000000204466022)↗

Repeatable and reproducible measurements of myocardial oxidative metabolism, blood flow and external efficiency using {sup 11}C-acetate PET

Background: Non-invasive approaches to investigate myocardial efficiency can help track the progression of heart failure (HF). This study evaluates the repeatability and reproducibility of {sup 11}C-acetate positron emission tomography (PET) imaging of oxidative metabolism. Methods and results: Dynamic {sup 11}C-acetate PET scans were performed at baseline and followup (47 ± 22 days apart) in 20 patients with stable HF with reduced ejection fraction. Two observers blinded to patients’ clinical data used FlowQuant{sup ®} to evaluate test–retest repeatability, as well as intra- and inter-observer reproducibility of {sup 11}C-acetate tracer uptake and clearance rates, for the measurement of myocardial oxygen consumption (MVO{sub 2}), myocardial external efficiency (MEE), work metabolic index (WMI), and myocardial blood flow. Reproducibility and repeatability were evaluated using intra-class-correlation (ICC) and Bland–Altman coefficient-of-repeatability (CR). Test–retest correlations and repeatability were better for MEE and WMI compared to MVO{sub 2}. All intra- and inter-observer correlations were excellent (ICC = 0.95-0.99) and the reproducibility values (CR = 3%-6%) were significantly lower than the test–retest repeatability values (22%-54%, P < 0.001). Repeatability was improved for all parameters using a newer PET–computed tomography (CT) scanner compared to older PET-only instrumentation. Conclusion: {sup 11}C-acetate PET measurements of WMI and MEE exhibited excellent test–retest repeatability and operator reproducibility. Newer PET–CT scanners may be preferred for longitudinal tracking of cardiac efficiency. [French] French Abstract: Contexte: Les examens non invasifs de la fonction myocardique aident à suivre la progression de l’insuffisance cardiaque. Dans ce travail, nous avons évalué la répétabilité et la reproductibilité de l’étude du métabolisme oxydatif du myocarde par imagerie tomographique à positrons avec l’acétate marqué au carbone 11. Méthodes et résultats: Une étude de base et un second examen TEP dynamique à l’ acétate marqué au carbone 11 ont été réalisés (47 ± 22 jours) chez 20 patients présentant une insuffisance cardiaque stable avec une fraction d’éjection réduite. Sans aucune connaissance des données cliniques et au moyen du programme FlowQuant®, deux observateurs ont évalué la répétabilité des TEPs de base et de leur suivi, la reproductibilité intra- et inter-observateur, l’absorption et la clearance du traceur, la mesure de la consommation d’oxygène du myocarde (MVO2), l’efficacité contractile du myocarde (MEE), l’index métabolique du travail myocardique (WMI) et le débit sanguin myocardique (MBF). La reproductibilité et la répétabilité ont été évaluées en utilisant la corrélation intra-classe (ICC) et le coefficient de répétabilité Altman (CR). Les corrélations entre les études de base et leur suivi et la répétabilité des données se sont avérées supérieures pour les paramètres MEE et WMI par rapport à MVO2. Toutes les corrélations intra- et inter-observateurs furent excellentes (ICC = 0,95-0,99). Les valeurs de reproductibilité (CR = 3-6%) furent significativement inférieures aux valeurs de répétabilité (22-54%, p <0.001). La répétabilité des paramètres mesurés s’est avérée supérieure avec un scanner TEP-TDM de nouvelle génération par rapport à l’utilisation de la TEP sans TDM Conclusion: Les mesures réalisées dans cette étude TEP 11C-acétate montre une excellent répétabilité et reproductibilité des paramètres WMI et WMI entre les examens de base et leur suivi effectués par des opérateurs différents. Les nouveaux scanners TEP-TDM devraient être préférés pour le suivi longitudinal de la fonction cardiaque. [Spanish] Spanish Abstract: Antecedentes: el abordaje no invasivo para investigar la eficiencia miocárdica puede ayudar en el seguimiento de la progresión de la insuficiencia cardíaca. Este estudio evalúa la repetibilidad y la reproducibilidad del estudio de metabolismo oxidativo con PET 11C-acetato. Métodos y resultados: Se realizaron estudios de PET 11C-acetato dinámicos al inicio y durante el seguimiento (47 ± 22 días de diferencia) en 20 pacientes con insuficiencia cardíaca estable y fracción de eyección reducida. Dos observadores cegados a los datos clínicos de los pacientes utilizaron FlowQuant® para evaluar la repetibilidad de la prueba-reprueba, así como la reproducibilidad intra e interobservador de la captación de radiotrazador 11C-acetato y sus tasas de eliminación, la medición del consumo miocárdico de oxígeno (MVO2), la eficiencia externa miocardica (EEM), el índice trabajo-metabólico (ITM) y flujo sanguíneo miocárdico (FSM). La reproducibilidad y la repetibilidad se evaluaron mediante la correlación intraclase (ICC) y el coeficiente de repetibilidad (CR) de Bland-Altman. Las correlaciones Prueba-Reprueba y la repetibilidad fueron mejores para la EEM y el ITM en comparación con el MVO2. Todas las correlaciones intra e interobservador fueron excelentes (ICC = 0.95-0.99) y los valores de reproducibilidad (CR = 3-6%) fueron significativamente menores que los valores de repetibilidad prueba-reprueba (22-54%, p <0.001). La repetibilidad fue mejor para todos los parámetros utilizando un equipo PET-TC más nuevo en comparación con un equipo PET sin CT. Conclusión: las mediciones del PET con 11C-acetato del ITM y EEM mostraron una excelente repetibilidad prueba-preprueba y reproducibilidad del operador. Los nuevos equipos PET-CT pueden ser elegidos para el seguimiento longitudinal de la eficiencia miocárdica. [Chinese] Chinese Abstract: 背景: 采用非侵入式方法来研究心肌代谢效率可以帮助追踪心力衰竭的过程。本研究评估利用碳-11 醋酸盐为 PET 显影剂行氧化代谢成像的可重复性和可再现性。 方法和结果: 纳入射血分数减低的 20 名稳定性心衰患者,对患者基线和 47±22 天随访都进行碳-11 醋酸盐 PET 扫描。为测量心肌耗氧量(MVO{sub 2}), 心肌外效率(MEE), 工作代谢指标(WMI)和心肌血流量(MBF), 两名观察者按照双盲的方法利用 FlowQuant®对碳-11 醋酸盐的摄取率和清空率进行了重复性测试以及不同观察者之间的可再现性测试。采用组内相关系数(ICC)和 Bland Altman 可重复性系数(CR)分别对可再现性和可重复性进行评估。MEE 和 WMI 的两次试验系数和可重复性优于MVO{sub 2}。所有观察者之间的相关系数都较好(ICC=0.95-0.99),可再现性系数的值(CR=3-6%)明显低于两次试验可重复性的值(22-54%, P<0.001)。相比于旧的只有 PET 的设备, 采用新型 PET-CT 扫描仪能够使所有参数的可再现性都有所提高。 结论: 碳-11醋酸盐 PET 显像测量 WMI 和 MEE 有很好的可重复性和可再现性。新的 PET-CT 扫描仪可能更适合于心脏代谢效率的长期追踪。.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Directional Assembly of Nanoparticles by DNA Shapes: Towards Designed Architectures and Functionality

In bottom–up self-assembly, DNA nanotechnology plays a vital role in the development of novel materials and promises to revolutionize nanoscale manufacturing technologies. DNA shapes exhibit many versatile characteristics, such as their addressability and programmability, which can be used for determining the organization of nanoparticles. Furthermore, the precise design of DNA tiles and origami provides a promising technique to synthesize various complex desired architectures. These nanoparticle-based structures with targeted organizations open the possibility to specific applications in sensing, optics, catalysis, among others. In this work, we review progress in the development and design of DNA shapes for the self-assembly of nanoparticles and discuss the broad range of applications for these architectures.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

An Analysis of FPGA LUT Bias and Entropy for Physical Unclonable Functions

Process variations within Field Programmable Gate Arrays (FPGAs) provide a rich source of entropy and are therefore well-suited for the implementation of Physical Unclonable Functions (PUFs). However, careful considerations must be given to the design of the PUF architecture as a means of avoiding undesirable localized bias effects that adversely impact randomness, an important statistical quality characteristic of a PUF. Here in this paper, we investigate a ring-oscillator (RO) PUF that leverages localized entropy from individual look-up table (LUT) primitives. A novel RO construction is presented that enables the individual paths through the LUT primitive to be measured and isolated at high precision, and an analysis is presented that demonstrates significant levels of localized design bias. The analysis demonstrates that delay-based PUFs that utilize LUTs as a source of entropy should avoid using FPGA primitives that are localized to specific regions of the FPGA, and instead, a more robust PUF architecture can be constructed by distributing path delay components over a wider region of the FPGA fabric. Compact RO PUF architectures that utilize multiple configurations within a small group of LUTs are particularly susceptible to these types of design-level bias effects. The analysis is carried out on data collected from a set of identically designed, hard macro instantiations of the RO implemented on 30 copies of a Zynq 7010 SoC.

97 MATHEMATICS AND COMPUTING↗

FPGA-Accelerated Machine Learning Inference as a Service for Particle Physics Computing

Large-scale particle physics experiments face challenging demands for high-throughput computing resources both now and in the future. New heterogeneous computing paradigms on dedicated hardware with increased parallelization, such as Field Programmable Gate Arrays (FPGAs), offer exciting solutions with large potential gains. The growing applications of machine learning algorithms in particle physics for simulation, reconstruction, and analysis are naturally deployed on such platforms. We demonstrate that the acceleration of machine learning inference as a web service represents a heterogeneous computing solution for particle physics experiments that potentially requires minimal modification to the current computing model. As examples, we retrain the ResNet-50 convolutional neural network to demonstrate state-of-the-art performance for top quark jet tagging at the LHC and apply a ResNet-50 model with transfer learning for neutrino event classification. Using Project Brainwave by Microsoft to accelerate the ResNet-50 image classification model, we achieve average inference times of 60 (10) ms with our experimental physics software framework using Brainwave as a cloud (edge or on-premises) service, representing an improvement by a factor of approximately 30 (175) in model inference latency over traditional CPU inference in current experimental hardware. A single FPGA service accessed by many CPUs achieves a throughput of 600–700 inferences per second using an image batch of one, comparable to large batch-size GPU throughput and significantly better than small batch-size GPU throughput. Deployed as an edge or cloud service for the particle physics computing model, coprocessor accelerators can have a higher duty cycle and are potentially much more cost-effective.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Challenges in Monte Carlo Event Generator Software for High-Luminosity LHC

Abstract We review the main software and computing challenges for the Monte Carlo physics event generators used by the LHC experiments, in view of the High-Luminosity LHC (HL-LHC) physics programme. This paper has been prepared by the HEP Software Foundation (HSF) Physics Event Generator Working Group as an input to the LHCC review of HL-LHC computing, which has started in May 2020.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Deep Generative Models for Fast Photon Shower Simulation in ATLAS

The need for large-scale production of highly accurate simulated event samples for the extensive physics programme of the ATLAS experiment at the Large Hadron Collider motivates the development of new simulation techniques. Building on the recent success of deep learning algorithms, variational autoencoders and generative adversarial networks are investigated for modelling the response of the central region of the ATLAS electromagnetic calorimeter to photons of various energies. The properties of synthesised showers are compared with showers from a full detector simulation using GEANT4 . Both variational autoencoders and generative adversarial networks are capable of quickly simulating electromagnetic showers with correct total energies and stochasticity, though the modelling of some shower shape distributions requires more refinement. This feasibility study demonstrates the potential of using such algorithms for ATLAS fast calorimeter simulation in the future and shows a possible way to complement current simulation techniques.

97 MATHEMATICS AND COMPUTING↗

Area-based composition predictions of materials fabricated using simultaneous wire-powder-directed energy deposition

Functionally graded materials are an emergent method for designing components with programmable site-specific material properties. These materials are typically fabricated using metal additive manufacturing tools by simultaneously feeding multiple wire and/or powder feedstocks at various rates to achieve spatial composition change. The wire-powder-directed energy deposition (WP-DED) technique is of particular interest for many functionally graded material applications by balancing the low raw materials cost of wire with the high resolution of powder. However, feeding wire and powder are inherently different processes since all extruded wire enters the melt pool, while much of the blown powder is scattered, which makes determining the composition of the build challenging. In this study, we devise a simple area-based measurement method for estimating the composition of WP-DED structures. WP-DED single beads are printed using 309L stainless steel wire and commercially pure Fe powder at five wire feed rates (0.5, 0.75, 1.00, 1.25, 1.50 mm/mm) and five powder feed rates (2, 4, 6, 8, 10 rpm). Characteristic defects including interface gaps and macrosegregation (lack of mixing) tendencies are examined. High powder feed rates (8, 10 rpm) result in interface gaps at all wire feed rates, but smooth deposition and complete mixing is achieved at low powder feed rates, particularly with lower wire feed rates as well. The area-based composition measurement method is within ±20% of energy dispersive x-ray spectroscopy measurements for all samples, showing its effectiveness as a rapid composition estimate for WP-DED materials development.

36 MATERIALS SCIENCE↗

Gas pore correlations in laser powder bed fusion of Al6061

Additive manufacturing (AM) of metal materials based on powder bed fusion technology is widely used now in many industries. A known limitation of this type of manufacturing is the formation of gas pores in the bulk material. Here we present a combined X-ray imaging and mid-infrared pyrometry study of pore formation in side-by-side tracks of Al6061 for different processing conditions using both in-situ and post-processing analysis. By carefully quantifying the distributions and correlations of pore positions, we show that an existing pore in one track often catalyzes the formation of another pore in an adjacent track. In a raster scan strategy commonly used to construct bulk material, this phenomenon has the result of forming subsurface perforations, or lines of pores transverse to the scanning direction in a rastered patch. If controlled, this effect can be eliminated to improve the yield strength of the build, or exploited to create programmable failures for specific purposes.

36 MATERIALS SCIENCE↗

Towards gradient multimaterial toolpath generation for direct ink writing with connected fermat spirals

This work describes advances towards a reproducible, parametrically defined algorithm for generating graded multimaterial toolpaths for direct ink writing. Expanding on the existing Fermat space-filling algorithm and coupling with image-driven processing techniques, we demonstrate the fabrication of multimaterial structures. Here, material composition is encoded within toolpaths by parsing hue values from a multi-colored image. By performing dynamic velocity compensation based on local curvature and Euclidean distance filtering, internal voids are mitigated while optimizing print fidelity. Here, the work opens new avenues for designing complex toolpaths with locally programmable composition.

3D Printing↗

Network of networks: Time series clustering of AmeriFlux sites

Environmental observation networks, such as AmeriFlux, are foundational for monitoring ecosystem response to climate change, management practices, and natural disturbances; however, their effectiveness depends on their representativeness for the regions or continents. We proposed an empirical, time series approach to quantify the similarity of ecosystem fluxes across AmeriFlux sites. We extracted the diel and seasonal characteristics (i.e., amplitudes, phases) from carbon dioxide, water vapor, energy, and momentum fluxes, which reflect the effects of climate, plant phenology, and ecophysiology on the observations, and explored the potential aggregations of AmeriFlux sites through hierarchical clustering. While net radiation and temperature showed latitudinal clustering as expected, flux variables revealed a more uneven clustering with many small (number of sites < 5), unique groups and a few large (> 100) to intermediate (15–70) groups, highlighting the significant ecological regulations of ecosystem fluxes. Many identified unique groups were from under-sampled ecoregions and biome types of the International Geosphere-Biosphere Programme (IGBP), with distinct flux dynamics compared to the rest of the network. At the finer spatial scale, local topography, disturbance, management, edaphic, and hydrological regimes further enlarge the difference in flux dynamics within the groups. Nonetheless, our clustering approach is a data-driven method to interpret the AmeriFlux network, informing future cross-site syntheses, upscaling, and model-data benchmarking research. Finally, we highlighted the unique and underrepresented sites in the AmeriFlux network, which were found mainly in Hawaii and Latin America, mountains, and at under-sampled IGBP types (e.g., urban, open water), motivating the incorporation of new/unregistered sites from these groups.

54 ENVIRONMENTAL SCIENCES↗

A framework for estimating the energy-saving potential of occupant behaviour improvement

Energy-related occupant behaviour in buildings has demonstrated considerable energy-saving potential. However, the current modelling method of occupant behaviour does not give sufficient considerations on the implementation difficulty of behaviour and provide a holistic map from survey data to various behaviour models. This article proposes a holistic survey-and-simulation-based framework for estimating the energy-saving potential of occupant behaviour improvement. In the framework, seven typical categories of occupant behaviour models are identified based on the survey results. According to the implementation difficulty, the models are integrated into four behaviour styles (baseline, wasteful, moderate and austere) to represent different levels of energy-saving consciousness of occupants. Based on a case study with a nationwide survey in Singapore, there are remarkable energy savings potential if occupant behaviour is improved; the building energy consumption can be reduced by up to 9.5% with the moderate behaviour improvement, and up to 21.0% with the aggressive behaviour improvement. The simulation results accord well with the measured results within a reasonable range of deviation. The framework can be applied to estimate the energy-saving potential of occupant behaviour improvement in a building with affordable cost, and the findings can inform a behaviour improvement programme with effective and efficient measures.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Advances in benchmarking and round robin testing for PEM water electrolysis: Reference protocol and hardware

While the number of publications in the PEM water electrolysis community increases each year, no common ground concerning reference hardware (test cells and test bench) and testing protocols has been yet established. This would, however, be necessary for the comparability of experimental results. First attempts for such reference hardware and procedures have been made in the framework of the Task 30 Electrolysis within the Technology Collaboration Programme on Advanced Fuel Cells (AFC TCP) of the International Energy Agency (IEA). Since then, improvements of both the test hardware (test cell and components) as well as the measurement protocol were identified, and a revised methodology and key results based on a comprehensive measurement series have been obtained. A detailed protocol for testing commercial reference components with a reference laboratory test cell developed in-house by Fraunhofer ISE is presented. For evaluation of the protocol and the hardware, it was tested at three different institutions at the same time. Impedance spectroscopic and polarization data was acquired and analyzed. The obtained differences in performance were calculated to give the community an expectation window to compare own data to. Finally, the importance of a thorough temperature control and the conditioning phase are demonstrated.

08 HYDROGEN↗

Experimental investigation of advanced turbine control strategies and load-mitigation measures with a model-scale floating offshore wind turbine system

To advance the control co-design of offshore wind energy systems, the authors perform basin-scale experiments with a fully instrumented and actuated floating offshore wind turbine model. The model consists of a 1:70 scale performance-matched model of the International Energy Agency Wind Technology Collaboration Programme 15-MW reference turbine atop the VolturnUS-S semisubmersible platform. The Reference OpenSource Controller provides real-time blade pitch and generator torque control. Here we aim to develop an open data set for the validation of numerical models in predicting the influence of turbine control and load-mitigation measures. For this purpose, we measure the effects of advanced turbine control features, including peak shaving and floating feedback as well as hull-based control using tuned mass dampers on the system. Overall, the results demonstrate measurable and consistent influences from the control and load-mitigation measures, thus confirming the usefulness as a validation data set. Peak shaving attenuates the response to wind turbulence at near-rated wind speed. Floating feedback reduces the load and platform pitch motion associated with the negative damping induced by blade pitch control. The tuned mass dampers also attenuate the system response near the targeted frequencies under suitable conditions. We also identify detrimental side effects of each load-mitigation measure.

17 WIND ENERGY↗

Low-power anisotropic molecular electronic memristors

A molecular electronic memristor, programmable resistive memory device, promises to revolutionize next-generation flexible data storage units, offering fast, dense and ultralow power solutions. Here we report anisotropic resistive switching in molecular κ-(BEDT-TTF) 2 Cu[N(CN) 2 ]Cl memristors, consisting of alternatively segregated bis(ethylenedithio)tetrathiafulvalene (BEDT-TTF) and Cu[N(CN) 2 ]Cl layers. Electron resistance switching behavior controlled by charge tunneling in molecular memristors show a low set voltage of 0.5 V (10 V/cm) with the ON/OFF ratio of 2.3×10 3 along a-axis and a high-level endurance of 1.25×10 4 cycles along all axes. Finally, the findings of such molecular electronic crystals promise for low-power data storage memristors.

36 MATERIALS SCIENCE↗

In vivo gene correction with targeted sequence substitution through microhomology-mediated end joining

Highlights: • A novel microhomology mediated end joining (MMEJ) gene correction method was tested. • MMEJ resulted in precise targeted sequence substitution (TSS) in vitro and in vivo. • MMEJ-TSS showed superior efficiency than homology-directed repair (HDR) in vitro. • MMEJ-TSS resulted in the survival of mice model of hereditary tyrosinemia in vivo. • MMEJ-TSS could overcome the limitations of HDR for gene therapy. Genome editing technology using programmable nucleases has rapidly evolved in recent years. The primary mechanism to achieve precise integration of a transgene is mainly based on homology-directed repair (HDR). However, an HDR-based genome-editing approach is less efficient than non-homologous end-joining (NHEJ). Recently, a microhomology-mediated end-joining (MMEJ)-based transgene integration approach was developed, showing feasibility both in vitro and in vivo. We expanded this method to achieve targeted sequence substitution (TSS) of mutated sequences with normal sequences using double-guide RNAs (gRNAs), and a donor template flanking the microhomologies and target sequence of the gRNAs in vitro and in vivo. Our method could realize more efficient sequence substitution than the HDR-based method in vitro using a reporter cell line, and led to the survival of a hereditary tyrosinemia mouse model in vivo. The proposed MMEJ-based TSS approach could provide a novel therapeutic strategy, in addition to HDR, to achieve gene correction from a mutated sequence to a normal sequence.

60 APPLIED LIFE SCIENCES↗

Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning

Regulation of chromatin structure is essential for controlling access of DNA to factors that require association with specific DNA sequences. Here we describe the development and validation of engineered chromatin remodeling proteins (E-ChRPs) for inducing programmable changes in nucleosome positioning by design. We demonstrate that E-ChRPs function both in vitro and in vivo to specifically reposition target nucleosomes and entire nucleosomal arrays. We show that induced, systematic positioning of nucleosomes over yeast Ume6 binding sites leads to Ume6 exclusion, hyperacetylation, and transcriptional induction at target genes. We also show that programmed global loss of nucleosome-free regions at Reb1 targets is generally inhibitory with mildly repressive transcriptional effects. E-ChRPs are compatible with multiple targeting modalities, including the SpyCatcher and dCas9 moieties, resulting in high versatility and enabling diverse future applications. Thus, engineered chromatin remodeling proteins represent a simple and robust means to probe and disrupt DNA-dependent processes in different chromatin contexts.

59 BASIC BIOLOGICAL SCIENCES↗