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At least 631 records · Page 35

A Prediction Method for Catchment Efficiency Loss due to Coaxial Nozzle Wear in Powder Fed Directed Energy Deposition Systems

Abstract Powder fed laser directed energy deposition systems show significant promise and their widespread adoption could greatly advance manufacturing technology; however, a significant amount of gas atomized metal powder is wasted during material deposition. As contaminated powder must be collected and disposed of as hazardous waste, this process is often criticized for its low catchment efficiency. This presents potential implementation and scaling issues, as widespread use of this technology would directly increase the amount of contaminated powder in need of safe disposal. A direct contribution to this waste issue was identified in past work as wearing exterior and interior surfaces on a replaceable nozzle component within the additive head of such a system integrated into a hybrid manufacturing machine tool. A computational fluid dynamics simulation is developed specifically for use within the manufacturing process by predicting catchment efficiency losses before a deposition operation is performed. The model is robust enough to calculate a catchment efficiency estimate within a reasonable transition time before deposition and is designed to replace visual estimation of nozzle deterioration by the machine operator. Both of two previously identified wear modes are represented in the simulation. Their effects on powder stream geometry are discussed in detail and the results are compared with in-situ measurements of powder stream geometry and concentrations. The resulting work contributes to the growing understanding of using prediction and prevention methods on catchment efficiency related part defects within these systems.

DeWitte, Lisa↗

Nanoporous weakly coordinating anionic frameworks (Final Technical Report)

Under this award, we synthesized and characterized new weakly coordinating, anionic covalent organic frameworks. The motivation was to expand the class of covalent organic frameworks though the introduction of the first weakly coordinating anionic ones. The significance of the weakly coordinating anionic character of these frameworks is associated with the character of the counter (metal) cations in their pores. Those counter-cations, due to the inability to effectively coordinate to the pore walls, have a “naked”, and thus highly electrophilic, Lewis acidic character. Such properties are expected to translate to a number of interesting physical properties that can be potentially used for a range of energy-relevant applications. One of these applications is gas adsorption, separation, and storage. The electrophilic, Lewis acidic character of the counter-cations are expected to strongly bind to gas molecules entering the pores leading to higher gas sorption capacities. Other applications include heterogeneous catalysis, ion exchange, and solid state ion conduction. Within the project we explored a range of chemical blocks, and tested synthesis conditions to polymerize these building blocks to form the target materials. In particular, we focused on materials with group 15 elements like phosphorus in the oxidation state +5 and the coordination number 6, that have a formal -1 charge. The synthesis of such materials is challenging because its success depends on the absence of residual monomeric and oligomeric side-products in the pores, and the absence of significant framework interpenetration. Crystalline forms of these materials require sufficient reversibility of the polymerization reaction (which is difficult to achieve because group 15 elements like P tend to make strong covalent bonds with neighbored elements), as well as suitable polymerization rates that prevent the formation of kinetically controlled products. We had success with the preparation of anionic porous organic frameworks with anionic building blocks containing P(V)O6 octahedra synthesized through Yamamoto coupling reactions. These materials are non-crystalline because of the irreversible nature of the Yamamoto coupling reaction, but show porosity. The porosity and surface area can be significantly increased by co-reaction with electrostatically neutral co-reactants. Very high porosity and surface areas can be achieved when the materials are washed with hydrochloric acid. This method is commonly used to free products from Yamamoto coupling reactions from by-products. Indeed, this method removed by products from the pores of our materials, however it also led to the hydrolysis of the PO6 octahedra to form pending phosphonic acid groups (-PO3H)-groups in the frameworks (PA-POFs) which was actually not desired. Nonetheless, these materials showed high CO2 sorption capacities. In addition, they show extremely high (actually record) sorption capacities for the removal of a range of common micropollutants such as bisphenol A (BPA) and 4-nitrophenol in water. BPA is a wide-spread organic pollutant and a known endocrine disruptor. The maximum adsorption capacity of BPA at equilibrium is found to be as high as 3,366 mg g-1 by Langmuir adsorption model, which is more than 10 times greater than peer materials. The polymer also rapidly removes various other organic micropollutants with more than 90% removal efficiencies. In addition, the PA-POF material can be regenerated at least five times by mild washing using methanol without significant loss in removal efficiency. This is significant advantage over commonly used activated carbon materials (that are in Brita water faucet filters, for example). Comparison studies showed that only materials with the phosphonate groups show extreme sorption although the number of PA group is actually small according to solid state NMR and EDX data. More research would be needed to investigate why this is (a possibility is that the phosphonate groups have a multiplying effect in which a PA-induced initial adsorption leads to the adsorption of much more adsorbate). The extreme sorption capabilities can also be visually seen when colored adsorbates such as 4-nitrophenol are used, as the adsorption of the nitrobenzene leads to the decoloration of the solution. We have produced three short videos that illustrate the sorption capabilities compared to two peer materials (activated carbon from dismantled Brita water filters, and a electrostatically neutral, chemically related, porous organic polymer, respectively).

36 MATERIALS SCIENCE↗

US HL-LHC Accelerator Upgrade Project: MQXFA11 shipping incident report

The truck transporting the MQXFA11 magnet from LBNL to BNL was involved in an accident on 7/20/22. It was rear ended by another truck. Drivers were not injured. The main hit took place on the right back corner. The truck with the MQXFA11 magnet was towed to a tow yard in Rockdale, IL (~50 min drive from Fermilab). Subsequently, it was moved on another truck and moved to Fermilab. Fermilab employees added 3 accelerometers on the crate before it was moved on the new truck and attended all loading/unloading operations at the tow yard and at FNAL. The magnet arrived at FNAL on July 28 th . Upon arrival a visual inspection was performed. Accelerometers were removed and shock data were analyzed. Electrical checkout and a metrology survey were carried out. Strain data were also collected from the fiber optics installed on two coils and compared with data obtained before shipment. This report presents a summary of results. More pictures and details can be found at: https://indico.fnal.gov/event/55698/

43 PARTICLE ACCELERATORS↗

MQXFA11 shipping incident report

The truck transporting the MQXFA11 magnet from LBNL to BNL was involved in an accident on 7/20/22. It was rear ended by another truck. The magnet arrived at FNAL on July 28th. Upon arrival a visual inspection was performed. Accelerometers were removed and shock data were analyzed. Electrical checkout and a metrology survey were carried out. Strain data were also collected from the fiber optics installed on two coils and compared with data obtained before shipment. This report presents a summary of results.

43 PARTICLE ACCELERATORS↗

Potential Role of Malassezia restricta in Pterygium Development

Pterygium is a condition affecting the ocular surface, marked by a triangular-shaped growth of fibrotic tissue extending from the nasal conjunctiva toward the corneal center, potentially causing visual impairment. While ultraviolet (UV )light exposure is the primary risk factor for pterygium, its underlying cause remains unclear. In order to better understand the true genesis of pterygium development, we investigated pterygium tissue and compared it with healthy conjunctiva controls. Given the eye’s direct environmental exposure, we analyzed the microbiota composition using metagenomic sequencing of pterygium tissue to identify microbes potentially associated with this condition. Metagenomic sequencing revealed a higher prevalence of the fungus Malassezia restricta in five pterygium samples, confirmed by in situ hybridization. The CHIT1 gene, which plays a role in antifungal defenses, displayed the highest expression in five pterygium tissue samples compared to healthy conjunctiva controls, suggesting the potential involvement of Malassezia restricta in pterygium development. Gene expression profiling of pterygium highlighted an IL-33 and IL-4 gene expression signature, along with an increased presence of M2 macrophages, emphasizing their role in promoting fibrosis—a hallmark feature of pterygium. The detection of Malassezia restricta in the pterygium samples and associated molecular changes provides novel insights into the ocular microbiome and raises the possibility of Malassezia’s involvement in pterygium pathology.

60 APPLIED LIFE SCIENCES↗

Big Data Framework with Machine Learning for D and D Applications - 19108

The nuclear industry is experiencing a steady increase in maintenance costs even though plants are maintained under high levels of safety, capability and reliability. Nuclear power plants are expected to run every unit at maximum capacity at all times, efficiently utilizing assets with minimal downtime. Surveillance and maintenance of nuclear decommissioning infrastructure provides lot challenges with respect to maintenance or decommissioning of the buildings. There is a need for a framework to analyze the huge amount of data generated by the sensors on the nuclear reactor components as well as structures, to monitor the conditions of these building over a period of time. Emerging technologies such as big data analytics have become a requirement in the nuclear industry to improve structural health monitoring and diagnostics. FIU will make use of existing mature technologies in the areas of imaging, robotics, big data, and machine learning/deep learning to assess the structural integrity of aging facilities at DOE sites. As these facilities await decommissioning, there is a need to understand the structural health of these structures. Many of these facilities were built over 50 years ago and in some cases these facilities have gone beyond the operational life expectancy. In other cases, the facilities have been placed in a state of 'cold and dark' and they are sitting unused, awaiting decommissioning. Finally, some older facilities are one-of-a-kind operational/production facilities supporting critical DOE missions and cannot be shut down. In any of these scenarios, the structural integrity of these facilities may be compromised, so it is imperative that adequate inspections and data collection/analysis be performed on a continuous and ongoing basis. The primary goals of the research include collecting various formats of data such as structured, unstructured and streaming data from the various sensors deployed in buildings, collect videos/pictures from various imaging sources, ingest them using a Hadoop distributed file system and process the data using Spark to perform batch processing and real time analytics. Research and development on various machine learning/deep learning algorithms will also be performed to analyze the heterogeneous data collected from nuclear decommission infrastructure. FIU will design the big data framework to ingest, store and process huge amounts of heterogeneous data collected from many sources and optimize the algorithms to provide insights into the data and predict anomalies observed when compared against baseline conditions. Various modules of this framework will include heterogeneous data sources, message broker, Hadoop distributed file system, Spark for stream and batch processing, machine learning/ deep learning, Cassandra - persistent data store and visualization. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Direct Visualization of Catalytically Active Sites at the FeO-Pt(111) Interface

Within the area of surface science, one of the “holy grails” is to directly visualize a chemical reaction at the atomic scale. Whereas this goal has been reached by high-resolution scanning tunneling microscopy (STM) in a number of cases for reactions occurring at flat surfaces, such a direct view is often inhibited for reaction occurring at steps and interfaces. Here we have studied the CO oxidation reaction at the interface between ultrathin FeO islands and a Pt(111) support by in situ STM and density functional theory (DFT) calculations. Time-lapsed STM imaging on this inverse model catalyst in O2 and CO environments revealed catalytic activity occurring at the FeO-Pt(111) interface and directly showed that the Fe-edges host the catalytically most active sites for the CO oxidation reaction. This is an important result since previous evidence for the catalytic activity of the FeO-Pt(111) interface is essentially based on averaging techniques in conjunction with DFT calculations. The presented STM results are in accord with DFTþU calculations, in which we compare possible CO oxidation pathways on oxidized Fe-edges and O-edges. We found that the CO oxidation reaction is more favorable on the oxidized Fe-edges, both thermodynamically and kinetically.

Environmental Molecular Sciences Laboratory↗

On the Importance of Chemical Precision in Organic Electronics: Fullerene Intercalation in Perfectly Alternating Conjugated Polymers

Abstract The true structure of alternating conjugated polymers—the state‐of‐the‐art materials for many organic electronics—often deviates from the idealized picture. Homocoupling defects are in fact inherent to the widely used cross‐coupling polymerization methods. Nevertheless, many polymers still perform excellently in the envisaged applications, which raises the question if one should really care about these imperfections. This article looks at the relevance of chemical precision (and lack thereof) in conjugated polymers covering the entire spectrum from the molecular scale, to the micro and mesostructure, up to the device level. The different types of polymerization errors for the alkoxylated variant of the benchmark (semi)crystalline polymer poly[2,5‐bis(3‐tetradecylthiophen‐2‐yl)thieno[3,2‐ b ]thiophene (PBTTT) are identified, visualized, and quantified and a general strategy to avoid homocoupling is introduced. Through a combination of experiments and supported by simulations, it is shown that these coupling defects hinder fullerene intercalation and limit device performance as compared to the homocoupling‐free analog. This clearly demonstrates that structural defects do matter and should be generally avoided, in particular when the geometrical regularity of the polymer is essential. These insights likely go beyond the specific PBTTT derivatives studied here and are of general relevance for the wider organic electronics field.

36 MATERIALS SCIENCE↗

Experimental study and discrete element method simulation of Geldart Group A particles in a small-scale fluidized bed

Geldart Group A particles are of great importance in various chemical processes because of advantages such as ease of fluidization, large surface area, and many other unique properties. It is very challenging to model the fluidization behavior of such particles as widely reported in the literature. In this study, a pseudo-2D experimental column with a width of 5 cm, a height of 45 cm, and a depth of 0.32 cm was developed for detailed measurements of fluidized bed hydrodynamics of fine particles to facilitate the validation of computational fluid dynamic (CFD) modeling. The hydrodynamics of sieved FCC particles (Sauter mean diameter of 148 µm and density of 1300 kg/m3) and NETL-32D sorbents (Sauter mean diameter of 100 µm and density of 480 kg/m3) were investigated mainly through the visualization by a high-speed camera. Numerical simulations were then conducted by using NETL’s open source code MFIX-DEM. Both qualitative and quantitative information including bed expansion, bubble characteristics, and solid movement were compared between the numerical simulations and the experimental measurement. Furthermore, the cohesive van der Waals force was incorporated in the MFIX-DEM simulations and its influences on the flow hydrodynamics were studied.

42 ENGINEERING↗

Visualization of post-detonation fireball flowfields and comparison to CFD modeling

Visualization of flow structures within post-detonation fireballs has been performed for benchmark validation of numerical simulations. Custom pressed PETN explosives with a 12-mm diameter hemispherical form factor were used to produce a spherically symmetric post-detonation flow with low soot yield. Hydroxyl-radical planar laser induce fluorescence (OH-PLIF) was employed to visualize the structure ranging from approximately 10 μs to 35 μs after shock breakout from the explosive pellet. Fireball simulations were performed using the HyBurn Computational Fluid Dynamics (CFD) package. Experimental OH-PLIF results were compared to synthetic OH-PLIF from post-processing of CFD simulations. From the comparison of experimental and synthetic OH-PLIF images, CFD is shown to replicate much of the flow structure observed in the experiments, revealing potential differences in turbulent length scales and OH kinetics. Furthermore, results provide significant advancement in experimental resolution of these harsh turbulent combustion environments and validate physical models thereof.

Detonator↗

Interfacial stabilization for inverted perovskite solar cells with long-term stability

Perovskite solar cells (PSCs) commonly exhibit significant performance degradation due to ion migration through the top charge transport layer and ultimately metal electrode corrosion. Here, we demonstrate an interfacial management strategy using a boron chloride subphthalocyanine (Cl 6 SubPc)/fullerene electron-transport layer, which not only passivates the interfacial defects in the perovskite, but also suppresses halide diffusion as evidenced by multiple techniques, including visual element mapping by electron energy loss spectroscopy. As a result, we obtain inverted PSCs with an efficiency of 22.0% (21.3% certified), shelf life of 7000 h, Τ 80 of 816 h under damp heat stress (compared to less than 20 h without Cl 6 SubPc), and initial performance retention of 98% after 2000 h at 80 °C in inert environment, 90% after 2034 h of illumination and maximum power point tracking in ambient for encapsulated devices and 95% after 1272 h outdoor testing ISOS-O-1. Our strategy and results pave a new way to move PSCs forward to their potential commercialization solidly.

14 SOLAR ENERGY↗

Influence of crystal allomorph and crystallinity on the products and behavior of cellulose during fast pyrolysis

Here, cellulose is the primary biopolymer responsible for maintaining the structural and mechanical integrity of cell walls and, during the fast pyrolysis of biomass, may be restricting cell wall expansion and inhibiting phase transitions that would otherwise facilitate efficient escape of pyrolysis products. Here, we test whether modifications in two physical properties of cellulose, its crystalline allomorph and degree of crystallinity, alter its performance during fast pyrolysis. We show that both crystal allomorph and relative crystallinity of cellulose impact the slate of primary products produced by fast pyrolysis. For both cellulose-I and cellulose-II, changes in crystallinity dramatically impact the fast pyrolysis product portfolio. In both cases, only the most highly crystalline samples produced vapors dominated by levoglucosan. Cellulose-III, on the other hand, produces largely the same slate of products regardless of its relative crystallinity and produced as much or more levoglucosan at all crystallinity levels compared to cellulose-I or II. In addition to changes in products, the different cellulose allomorphs affected the viscoelastic properties of cellulose during rapid heating. Real-time hot-stage pyrolysis was used to visualize the transition of the solid material through a molten phase and particle shrinkage. SEM analysis of the chars revealed additional differences in viscoelastic properties and molten phase behavior impacted by cellulose crystallinity and allomorph. Regardless of relative crystallinity, the cellulose-III samples displayed the most obvious evidence of having transitioned through a molten phase.

09 BIOMASS FUELS↗

Three-dimensional imaging of mitochondrial cristae complexity using cryo-soft X-ray tomography

Mitochondria are dynamic organelles that change morphology to adapt to cellular energetic demands under both physiological and stress conditions. Cardiomyopathies and neuronal disorders are associated with structure-related dysfunction in mitochondria, but three-dimensional characterizations of the organelles are still lacking. In this study, we combined high-resolution imaging and 3D electron density information provided by cryo-soft X-ray tomography to characterize mitochondria cristae morphology isolated from murine. Using the linear attenuation coefficient, the mitochondria were identified (0.247 ± 0.04 µm -1 ) presenting average dimensions of 0.90 ± 0.20 µm in length and 0.63 ± 0.12 µm in width. The internal mitochondria structure was successfully identified by reaching up the limit of spatial resolution of 35 nm. The internal mitochondrial membranes invagination (cristae) complexity was calculated by the mitochondrial complexity index (MCI) providing quantitative and morphological information of mitochondria larger than 0.90 mm in length. The segmentation to visualize the cristae invaginations into the mitochondrial matrix was possible in mitochondria with MCI ≥ 7. Altogether, we demonstrated that the MCI is a valuable quantitative morphological parameter to evaluate cristae modelling and can be applied to compare healthy and disease state associated to mitochondria morphology.

3-D reconstruction↗

TH-A-19A-01: An Open Source Software for Proton Treatment Planning in Heterogeneous Medium

Purpose: Due to its success in Radiation Oncology during the last decade, interest in proton therapy is on the rise. Unfortunately, despite the global enthusiasm in the field, there is presently no free, multiplatform and customizable Treatment Planning System (TPS) providing proton dose distributions in heterogenous medium. This restricts substantially the progress of clinical research for groups without access to a commercial Proton TPS. The latest implementation of our pencil beam dose calculation algorithm for proton beams within the 3D Slicer open-source environment fulfills all the conditions described above. Methods: The core dose calculation algorithm is based on the Hong algorithm (1), which was upgraded with the Kanematsu theory describing the evolution of the lateral scattering of proton beamlets in heterogeneous medium. This algorithm deals with both mono-energetic beams and Spread Out Bragg Peak (SOBP). In order to be user-friendly, we provide a graphical user interface implemented with the Qt libraries, and visualization with the 3D Slicer medical image analysis software. Two different pencil beam algorithms were developed, and the clinical proton beam line at our facility was modeled. Results: The dose distributions provided by our algorithms were compared to dose distributions coming from both commercialized XiO TPS and literature (dose measurements, GEANT4 and MCNPx) and turned out to be in a good agreement, with maximum dose discrepancies of 5% in homogeneous phantoms and 10% in heterogeneous phantoms. The algorithm of SOBP creation from an optimized weigthing of mono-energetic beams results in flat SOBP. Conclusion: We hope that our efforts in implementing this new, open-source proton TPS will help the research groups to have a free access to a useful, reliable proton dose calculation software.(1) L. Hong et al., A pencil beam algorithm for proton dose calculations, Phys. Med. Biol. 41 (1996) 1305–1330. This project is paid for by NCI/MGH Federal share as a research grant.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

SU-G-206-05: A Comparison of Head Phantoms Used for Dose Determination in Imaging Procedures

Purpose: To determine similarities and differences between various head phantoms that might be used for dose measurements in diagnostic imaging procedures. Methods: We chose four frequently used anthropomorphic head phantoms (SK-150, PBU-50, RS-240T and Alderson Rando), a computational patient phantom (Zubal) and the CTDI head phantom for comparison in our study. We did a CT scan of the head phantoms using the same protocol and compared their dimensions and CT numbers. The scan data was used to calculate dose values for each of the phantoms using EGSnrc Monte Carlo software. An .egsphant file was constructed to describe these phantoms using a Visual C++ program for DOSXYZnrc/EGSnrc simulation. The lens dose was calculated for a simulated CBCT scan using DOSXYZnrc/EGSnrc and the calculated doses were validated with measurements using Gafchromic film and an ionization chamber. Similar calculations and measurements were made for PA radiography to investigate the attenuation and backscatter differences between these phantoms. We used the Zubal phantom as the standard for comparison since it was developed based on a CT scan of a patient. Results: The lens dose for the Alderson Rando phantom is around 9% different than the Zubal phantom, while the lens dose for the PBU-50 phantom was about 50% higher, possibly because its skull thickness and the density of bone and soft tissue are lower than anthropometric values. The lens dose for the CTDI phantom is about 500% higher because of its totally different structure. The entrance dose profiles are similar for the five anthropomorphic phantoms, while that for the CTDI phantom was distinctly different. Conclusion: The CTDI and PBU-50 head phantoms have substantially larger lens dose estimates in CBCT. The other four head phantoms have similar entrance dose with backscatter hence should be preferred for dose measurement in imaging procedures of the head. Partial support from NIH Grant R01-EB002873 and Toshiba Medical Systems Corp.

60 APPLIED LIFE SCIENCES↗

SU-G-JeP2-12: Quantification of 3D Geometric Distortion for 1.5T and 3T MRI Scanners Used for Radiation Therapy

Purpose: To quantify the magnitude of geometric distortion for MRI scanners and provide recommendations for MRI imaging for radiation therapy Methods: A novel phantom, QUASAR MRID3D [Modus Medical Devices Inc.], was scanned to evaluate the level of 3D geometric distortion present in five MRI scanners used for radiation therapy in our department. The phantom was scanned using the body coil with 1mm image slice thickness to acquire 3D images of the phantom body. The phantom was aligned to its geometric center for each scan, and the field of view was set to visualize the entire phantom. The dependence of distortion magnitude with distance from imaging isocenter and with magnetic field strength (1.5T and 3T) was investigated. Additionally, the characteristics of distortion for Siemens and GE machines were compared. The image distortion for each scanner was quantified in terms of mean, standard deviation (STD), maximum distortion, and skewness. Results: The 3T and 1.5T scans show a similar absolute distortion with a mean of 1.38mm (0.33mm STD) for 3T and 1.39mm (0.34mm STD) for 1.5T for a 100mm radius distance from isocenter. Some machines can have a distortion larger than 10mm at a distance of 200mm from the isocenter. The distortions are presented with plots of the x, y, and z directional components. Conclusion: The results indicate that quantification of MRI image distortion is crucial in radiation oncology for target and organ delineation and treatment planning. The magnitude of geometric distortion determines the margin needed for target contouring which is usually neglected in treatment planning process, especially for SRS/SBRT treatments. Understanding the 3D distribution of the MRI image distortion will improve the accuracy of target delineation and, hence, treatment efficacy. MRI imaging with proper patient alignment to the isocenter is vital to reducing the effects of MRI distortion in treatment planning.

60 APPLIED LIFE SCIENCES↗

Degradation of Commercial Lithium-Ion Cells as a Function of Chemistry and Cycling Conditions

Energy storage systems with Li-ion batteries are increasingly deployed to maintain a robust and resilient grid and facilitate the integration of renewable energy resources. However, appropriate selection of cells for different applications is difficult due to limited public data comparing the most commonly used off-the-shelf Li-ion chemistries under the same operating conditions. This article details a multi-year cycling study of commercial LiFePO 4 (LFP), LiNi x Co y Al 1–x–y O 2 (NCA), and LiNi x Mn y Co 1–x–y O 2 (NMC) cells, varying the discharge rate, depth of discharge (DOD), and environment temperature. The capacity and discharge energy retention, as well as the round-trip efficiency, were compared. Even when operated within manufacturer specifications, the range of cycling conditions had a profound effect on cell degradation, with time to reach 80% capacity varying by thousands of hours and cycle counts among cells of each chemistry. The degradation of cells in this study was compared to that of similar cells in previous studies to identify universal trends and to provide a standard deviation for performance. All cycling files have been made publicly available at batteryarchive.org, a recently developed repository for visualization and comparison of battery data, to facilitate future experimental and modeling efforts.

25 ENERGY STORAGE↗

FastProNGS: fast preprocessing of next-generation sequencing reads

Background Next-generation sequencing technology is developing rapidly and the vast amount of data that is generated needs to be preprocessed for downstream analyses. Yet, until now, software that can efficiently make all the quality assessments and filtration of raw data is still lacking. Results We developed FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest. Read information before and after filtration can be output in plain-text, JSON, or HTML formats with user-friendly visualization. Conclusions FastProNGS is a rapid, standardized, and user-friendly tool for preprocessing next-generation sequencing data within minutes. It is an all-in-one software that is convenient for bulk data analysis. It is additionally very flexible and can implement different functions using different user-set parameter combinations.

97 MATHEMATICS AND COMPUTING↗