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DOE OSTI2021

A Possible Neutron-Antineutron Oscillation Experiment at PF1B at the Institut Laue Langevin

We consider a possible neutron–antineutron ($n-\overline{n}$) oscillation experiment at the PF1B instrument at Institut Laue Langevin. It can improve the best existing constraint on the transition rate and also allow the testing of the methods and instrumentation which would be needed for a later larger-scale experiment at ESS. The main gain factors over the most competitive experiment, performed earlier at PF1 instrument at ILL, are: a more intense neutron beam and a new operating mode based on coherent n and $\overline{n}$ mirror reflections. The installation of such an experiment would need a temporary replacement of the existing ballistic neutron guide by a specially designed n/$\overline{n}$ guide with a gradually increasing cross section and a specially selected coating as well as the development and construction of an advanced $\overline{n}$ annihilation detector with a high efficiency and low background. The overall gain factor could reach up to an order of magnitude and depends on the chosen experiment configuration.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

NASA NTRSDate not supplied

Remote Sensing of Hail from Space: Retrievals, Climatologies, and Challenges Going Forward

In addition to the myriad threats that severe hailstorms pose to society, infrastructure and agriculture, severe hail is difficult to measure in situ, and surface-based hail reporting and detection methods are inconsistent and subject to geographical or societal biases. This motivates the use of spaceborne remote-sensing platforms to retrieve hail and construct climatologies in the most globally consistent way. Passive-microwave algorithms leverage the sensitivity of spaceborne passive-microwave radiometers to scattering by hail, particularly in the channels from 10 to 89 GHz. These retrievals are used to construct global climatologies of severe hail. The Bang and Cecil (2019) retrievals has been applied to several different spaceborne sensors: the Tropical Rainfall Measuring Mission (TRMM) Microwave Imager (TMI), Global Precipitation Measurement Mission (GPM) Microwave Imager, Advanced Microwave Scanning Radiometer for EOS (AMSR-E), and Advanced Microwave Scanning Radiometer 2 (AMSR2) sensors and used to construct [near] global climatologies of severe hail. This retrieval, and others, have been tested using Global Precipitation Measurement (GPM) Ku-band precipitation radar, to assess their effectiveness and regional variability. A successful retrieval and climatology are those that correspond tightly to radar reflectivity and give minimal appearance of regional biases, especially with latitude. Satellite platforms offer consistent observations, even in remote, data-sparse, and oceanic regions that ground-based networks exclude. There are, however, potential disconnects between the processes identified aloft by the satellite and the resultant weather at the ground, leading to uncertainties in the retrievals that may propagate into satellite-based climatologies, particularly in the Tropics, where there are abundant strong - but not necessarily hailing - storms that are strongly represented in the current satellite climatologies. There are ongoing efforts to assess and mitigate the contributing factors to these uncertainties, chiefly among them the effects of non-uniform beam filling in the passive-microwave footprint, and the relationships between the size distributions of hailstones aloft and the dynamic processes and environments with which they interact throughout their trajectories.

Sarah D Bang↗

NASA NTRSDate not supplied

Spaceborne Remote Sensing of Hail: Retrievals, Climatologies, and Challenges Going Forward

Sarah D Bang↗

NASA NTRS1989

Specialty functions singularity mechanics problems

The focus is in the development of more accurate and efficient advanced methods for solution of singular problems encountered in mechanics. At present, finite element methods in conjunction with special functions, boolean sum and blending interpolations are being considered. In dealing with systems which contain a singularity, special finite elements are being formulated to be used in singular regions. Further, special transition elements are being formulated to couple the special element to the mesh that models the rest of the system, and to be used in conjunction with 1-D, 2-D and 3-D elements within the same mesh. Computational simulation with a least squares fit is being utilized to construct special elements, if there is an unknown singularity in the system. A novel approach is taken in formulation of the elements in that: (1) the material properties are modified to include time, temperature, coordinate and stress dependant behavior within the element; (2) material properties vary at nodal points of the elements; (3) a hidden-symbolic computation scheme is developed and utilized in formulating the elements; and (4) special functions and boolean sum are utilized in order to interpolate the field variables and their derivatives along the boundary of the elements. It may be noted that the proposed methods are also applicable to fluids and coupled problems.

Sarigul, Nesrin↗

DOE OSTI2023

Construction and Commissioning of Gas Electron Multiplier (GEM) Detectors in Advanced Assembly Design for Low-Energy Applications at High Rates and Analysis of GEM Data From the Muse Experiment at PSI

The search beyond the Standard Model explores dark matter and a potential fifth force. DarkLight@ARIEL investigates the dark photon as a mediator between ordinary and dark matter. The experiment aims to measure the process e?Ta ? e?TaX ? e?Ta(e?e+), by detecting a charged lepton pair in the final state. The spectrometers will be instrumented with Gas Electron Multiplier (GEM) detectors with minimal material budget for tracking. A novel GEM construction technique is employed for fabricating 25 cm x 40 cm GEM detectors, where all layers are mechanically stretched and assembled within a double frame. The dissertation outlines physics motivation, methods, experimental setup, and the role of GEM detectors in DarkLight. A comprehensive discussion on GEM detectors, focusing on the "NS2" technique, including design, parts, assembly, testing, and performance evaluation will be discussed. The proton has garnered attention due to discrepancies in measuring its charge radius using muonic hydrogen and electron-based methods. The 2010 muonic hydrogen measurement of the proton charge radius Rp = 0.84184(67) fm, showed a significant 7? discrepancy compared to the previously known value of Rp = 0.8775(51) fm, giving rise to the proton radius puzzle. Through simultaneous measurements of e ? p and ? ? p elastic scattering, MUSE facilitates a precise and direct comparison of the proton radius. The physics background of the proton radius puzzle, measurement techniques, the approach adopted by the MUSE experiment, its significance and the experimental setup will be discussed. Furthermore, the role of GEM detectors, along with an in-depth analysis of their data and efficiency will be discussed and evaluated.

Mohammed Prem Nazeer, Sahara↗

DOE OSTI2026

Advancing Mass Timber Buildings: Novel Methods Improve Thermal Assessment and Material Use

For nearly a century, thermal demand calculations for buildings have relied on simplified models developed to match the technical constraints of their era. The first standards, introduced in Germany and Austria in 1929, established climate zones and material conductivity coefficients that, with only incremental updates, still underpin many current assessments. Yet, methods such as Hot box testing, originally designed for lightweight insulation, continue to be applied for mass timber buildings, overlooking thermodynamic characteristics confer real-world advantages. Recent research at Oak Ridge National Laboratory incorporates updated methodologies, aligned with ASHRAE Standard 55 (ASHRAE, 2023) accounting for factors such as thermal inertia, inner surface temperatures, emissivity, solar gains, and dynamic outdoor conditions. These factors better reflect observed heating and cooling loads and highlight opportunities for efficient use of materials in mass timber construction. This work provides a framework for designing comfortable, resilient, and resource-efficient buildings while aligning with performance expectations in energy codes.

Pickett, Robert [International Mass Timber Allianc↗

NASA NTRS1978

Recent advances in thermal-structural analysis and design

A continuing effort to develop a comprehensive capability for thermal-structural analysis and automated design (sizing) is reviewed. A principal role in the activity is played by the finite element program SPAR which contains both an efficient structural and thermal analysis capability. The benefit of having thermal and structural analyses in the same finite element program is illustrated by the application of SPAR to design calculations for the National Transonic Facility - a cryogenic wind tunnel under construction at Langley. Some experience with large-scale thermal structural analysis problems, particularly the space shuttle orbiter, has led to the identification of some analysis needs. Those needs include automated model generation and data output for lumped parameter thermal analysis, faster solution methods for nonlinear transient heat transfer, automated interpolation of temperature data from a thermal finite element model to a dissimilar structural finite model, and automated techniques to identify the times at which the critical combinations of transient heating and loads occur on a structure.

Adelman, H. M.↗

NASA NTRS1998

Integrated Task and Data Parallel Programming

This research investigates the combination of task and data parallel language constructs within a single programming language. There are an number of applications that exhibit properties which would be well served by such an integrated language. Examples include global climate models, aircraft design problems, and multidisciplinary design optimization problems. Our approach incorporates data parallel language constructs into an existing, object oriented, task parallel language. The language will support creation and manipulation of parallel classes and objects of both types (task parallel and data parallel). Ultimately, the language will allow data parallel and task parallel classes to be used either as building blocks or managers of parallel objects of either type, thus allowing the development of single and multi-paradigm parallel applications. 1995 Research Accomplishments In February I presented a paper at Frontiers 1995 describing the design of the data parallel language subset. During the spring I wrote and defended my dissertation proposal. Since that time I have developed a runtime model for the language subset. I have begun implementing the model and hand-coding simple examples which demonstrate the language subset. I have identified an astrophysical fluid flow application which will validate the data parallel language subset. 1996 Research Agenda Milestones for the coming year include implementing a significant portion of the data parallel language subset over the Legion system. Using simple hand-coded methods, I plan to demonstrate (1) concurrent task and data parallel objects and (2) task parallel objects managing both task and data parallel objects. My next steps will focus on constructing a compiler and implementing the fluid flow application with the language. Concurrently, I will conduct a search for a real-world application exhibiting both task and data parallelism within the same program. Additional 1995 Activities During the fall I collaborated with Andrew Grimshaw and Adam Ferrari to write a book chapter which will be included in Parallel Processing in C++ edited by Gregory Wilson. I also finished two courses, Compilers and Advanced Compilers, in 1995. These courses complete my class requirements at the University of Virginia. I have only my dissertation research and defense to complete.

Grimshaw, A. S.↗

DOE OSTI2022

Finding Electronic Structure Machine Learning Surrogates without Training

A myriad of phenomena in materials science and chemistry rely on quantum-level simulations of the electronic structure in matter. While moving to larger length and time scales has been a pressing issue for decades, such large-scale electronic structure calculations are still challenging despite modern software approaches and advances in high-performance computing. The silver lining in this regard is the use of machine learning to accelerate electronic structure calculations – this line of research has recently gained growing attention. The grand challenge therein is finding a suitable machine-learning model during a process called hyperparameter optimization. This, however, causes a massive computational overhead in addition to that of data generation. We accelerate the construction of machine-learning surrogate models by roughly two orders of magnitude by circumventing excessive training during the hyperparameter optimization phase. We demonstrate our workflow for Kohn-Sham density functional theory, the most popular computational method in materials science and chemistry.

36 MATERIALS SCIENCE↗

NASA NTRS1998

Integrated Task And Data Parallel Programming: Language Design

his research investigates the combination of task and data parallel language constructs within a single programming language. There are an number of applications that exhibit properties which would be well served by such an integrated language. Examples include global climate models, aircraft design problems, and multidisciplinary design optimization problems. Our approach incorporates data parallel language constructs into an existing, object oriented, task parallel language. The language will support creation and manipulation of parallel classes and objects of both types (task parallel and data parallel). Ultimately, the language will allow data parallel and task parallel classes to be used either as building blocks or managers of parallel objects of either type, thus allowing the development of single and multi-paradigm parallel applications. 1995 Research Accomplishments In February I presented a paper at Frontiers '95 describing the design of the data parallel language subset. During the spring I wrote and defended my dissertation proposal. Since that time I have developed a runtime model for the language subset. I have begun implementing the model and hand-coding simple examples which demonstrate the language subset. I have identified an astrophysical fluid flow application which will validate the data parallel language subset. 1996 Research Agenda Milestones for the coming year include implementing a significant portion of the data parallel language subset over the Legion system. Using simple hand-coded methods, I plan to demonstrate (1) concurrent task and data parallel objects and (2) task parallel objects managing both task and data parallel objects. My next steps will focus on constructing a compiler and implementing the fluid flow application with the language. Concurrently, I will conduct a search for a real-world application exhibiting both task and data parallelism within the same program m. Additional 1995 Activities During the fall I collaborated with Andrew Grimshaw and Adam Ferrari to write a book chapter which will be included in Parallel Processing in C++ edited by Gregory Wilson. I also finished two courses, Compilers and Advanced Compilers, in 1995. These courses complete my class requirements at the University of Virginia. I have only my dissertation research and defense to complete.

Grimshaw, Andrew S.↗

DOE OSTI2024

Equilibrium core modeling of a pebble bed reactor similar to the Xe-100 with SCALE

As the nuclear industry moves towards licensing and constructing advanced reactors, new attention has been focused on the advanced reactor designs that have past operational experience, such as pebble-bed high-temperature gas-cooled reactors (PB-HTGRs). Pebble-bed reactor designs have many advantages, such as their higher operating temperatures and online refueling capabilities. However, high-fidelity computational modeling of pebble-bed reactor designs, from reactor startup to operation at equilibrium, is more challenging compared to conventionally fueled reactors due to the continuous movement of the fuel pebbles through the reactor during operation. In previous work at Oak Ridge National Laboratory (ORNL), the SCALE Leap-In method for Cores at Equilibrium (SLICE) was developed around tools within the SCALE code system. This iterative method can effectively generate pebble-bed reactor zone-wise fuel inventories at equilibrium core operation within a reasonable computational time. The objective of this work was to further verify the ORNL SLICE method and to investigate the impact of considering temperature profiles during the application of the method. The SLICE method was applied to a modular high-temperature gas-cooled reactor design based upon publicly available design specifications of the Xe-100 pebble-bed reactor. Upon comparing the results from the SLICE method to published literature, the differences in the eigenvalue k effective were on the order of several hundred pcm (percent millirho). To investigate one possible cause of these differences, a study looking at the sensitivity of the full-core equilibrium k effective and discharge nuclide inventory to temperature was performed by developing equilibrium cores of two additional temperature profiles. From this temperature study, differences on the order of hundreds of pcm for the full-core equilibrium k effective , and up to 15% difference for the discharge inventories were found. In conclusion, these results indicated the strong dependence on temperature that needs to be considered for future work in equilibrium modeling of PB-HTGRs.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2024

AI-assisted detector design for the EIC (AID(2)E)

Artificial Intelligence is poised to transform the design of complex, large-scale detectors like ePIC at the future Electron Ion Collider. Featuring a central detector with additional detecting systems in the far forward and far backward regions, the ePIC experiment incorporates numerous design parameters and objectives, including performance, physics reach, and cost, constrained by mechanical and geometric limits. This project aims to develop a scalable, distributed AI-assisted detector design for the EIC (AID(2)E), employing state-of-the-art multiobjective optimization to tackle complex designs. Supported by the ePIC software stack and using G EANT 4 simulations, our approach benefits from transparent parameterization and advanced AI features. The workflow leverages the PanDA and iDDS systems, used in major experiments such as ATLAS at CERN LHC, the Rubin Observatory, and sPHENIX at RHIC, to manage the compute intensive demands of ePIC detector simulations. Tailored enhancements to the PanDA system focus on usability, scalability, automation, and monitoring. Ultimately, this project aims to establish a robust design capability, apply a distributed AI-assisted workflow to the ePIC detector, and extend its applications to the design of the second detector (Detector-2) in the EIC, as well as to calibration and alignment tasks. Additionally, we are developing advanced data science tools to efficiently navigate the complex, multidimensional trade-offs identified through this optimization process.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Designing Cladded Components for High Temperature Nuclear Service: Part II—Design Rules

The challenge of using existing ASME Section III, Division 5, class A metallic materials for the construction of structural components of advanced reactors with corrosive coolants could be mitigated by allowing designers to use cladding to protect the base material from corrosion. However, the existing Section III, Division 5 rules provide no guidance on the evaluation of strain accumulation and creep-fatigue damage in cladded components. The availability of design rules for cladded components that do not require long-term clad material testing could promote the application of the cladding approach to accelerate the deployment schedule of these advanced reactor systems. To avoid long-term properties for the clad materials Part I of this work proposes two approximate design analysis methods for two types of clad materials—soft clads that creep much faster and have lower yield stress than the class A base material, and hard clads that creep much slower and have higher yield stress than the class A base material. The proposed analysis methods approximate the response of a soft clad by treating it as perfectly compliant and of a hard clad by treating it as linear elastic. Based on these approximate design analysis strategies this Part II develops a complete set of design rules for class A components cladded with either soft or hard clad materials. In conclusion, Part II discusses the reasoning behind the proposed design rules and uses example finite element analyses of representative reactor components to illustrate the use of these design methods.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

NASA NTRS2012

Forming Human-Robot Teams Across Time and Space

NASA pushes telerobotics to distances that span the Solar System. At this scale, time of flight for communication is limited by the speed of light, inducing long time delays, narrow bandwidth and the real risk of data disruption. NASA also supports missions where humans are in direct contact with robots during extravehicular activity (EVA), giving a range of zero to hundreds of millions of miles for NASA s definition of "tele". . Another temporal variable is mission phasing. NASA missions are now being considered that combine early robotic phases with later human arrival, then transition back to robot only operations. Robots can preposition, scout, sample or construct in advance of human teammates, transition to assistant roles when the crew are present, and then become care-takers when the crew returns to Earth. This paper will describe advances in robot safety and command interaction approaches developed to form effective human-robot teams, overcoming challenges of time delay and adapting as the team transitions from robot only to robots and crew. The work is predicated on the idea that when robots are alone in space, they are still part of a human-robot team acting as surrogates for people back on Earth or in other distant locations. Software, interaction modes and control methods will be described that can operate robots in all these conditions. A novel control mode for operating robots across time delay was developed using a graphical simulation on the human side of the communication, allowing a remote supervisor to drive and command a robot in simulation with no time delay, then monitor progress of the actual robot as data returns from the round trip to and from the robot. Since the robot must be responsible for safety out to at least the round trip time period, the authors developed a multi layer safety system able to detect and protect the robot and people in its workspace. This safety system is also running when humans are in direct contact with the robot, so it involves both internal fault detection as well as force sensing for unintended external contacts. The designs for the supervisory command mode and the redundant safety system will be described. Specific implementations were developed and test results will be reported. Experiments were conducted using terrestrial analogs for deep space missions, where time delays were artificially added to emulate the longer distances found in space.

Hambuchen, Kimberly↗

NASA NTRS2019

Reconstruction of the Advanced Supersonic Parachute Inflation Research Experiment Sounding Rocket Flight Tests with Strengthened Disk-Gap-Band Parachute

The Advanced Supersonic Parachute Inflation Research and Experiments project is a flight test program for development of supersonic parachutes for future use at Mars. The flight tests are a risk-reduction program for the Mars 2020 mission. The flight tests involve two Disk-Gap- Band parachute designs to be tested at relevant Mach number and dynamic pressure regimes for the Mars 2020 entry capsule. The first of these parachutes is a built-to-print design that was successfully employed by the Mars Science Laboratory lander at Mars in August 2012, and the second is a design that is strengthened in material properties and construction methods but has the same geometry as that used by Mars Science Laboratory. The first flight test of the built-to-print parachute took place on October 4, 2017 at NASA's Wallops Flight Facility. The parachute test was successful. The second and third flight tests took place on March 31st and September 7th 2018, respectively, and successfully tested the strengthened parachute design. This paper describes the instrumentation, data analysis techniques, and atmospheric and trajectory reconstruction results from the second and third flight tests.

Karlgaard, Christopher D.↗

NASA NTRS2018

Reconstruction of the Advanced Supersonic Parachute Inflation Research Experiment Sounding Rocket Flight Test

The Advanced Supersonic Parachute Inflation Research and Experiments project is a flight test program for development of supersonic parachutes for potential future use at Mars. The flight tests are designed to reduce risk for the Mars 2020 mission. The flight tests involve two Disk-Gap-Band parachute designs to be tested at relevant Mach number and dynamic pressure conditions for the Mars 2020 entry capsule. The first of these parachutes is a built-to-print design that was successfully employed by the Mars Science Laboratory lander at Mars in August 2012, and the second is a design that is strengthened in material properties and construction methods but has the same geometry as that used by Mars Science Laboratory. The first flight test of the built-to-print parachute took place on October 4, 2017 at NASA's Wallops Flight Facility. This paper describes the instrumentation, data analysis techniques, and atmospheric and trajectory reconstruction results from this flight test.

Karlgaard, Christopher D.↗

NASA NTRSDate not supplied

Shock-Wave/Boundary-Layer Interaction (SWBLI) Experiments in the Presence of Transition-to-Turbulence on a Flat Plate Model in the NASA LaRC 31-Inch Mach 10 Air Tunnel

Historically, there have been a limited number of studies involving Transitional Shock-Wave/Boundary-Layer Interactions (XSWBLI) in hypersonic flows, the majority of which have been performed at Mach Numbers of 7.5 and below. Additionally, there have been even fewer such experiments which incorporate non-intrusive and optical diagnostics. NASA Langley Research Center (NASA LaRC), in collaboration with The University of Texas at San Antonio (UTSA) and The University of Tennessee Space Institute (UTSI), is currently planning and preparing for a series of experimental aerodynamic tests using the NASA LaRC 31-inch Mach 10 Air Tunnel. The experiments will primarily focus on studying the dynamics of Shock-Wave/Boundary-Layer Interactions (SWBLI) in the presence of transition (XSWBLI) and turbulence (SWTBLI) on a large, flat plate model at a freestream Mach number of 10. Besides continued interest in understanding the flow at high Mach numbers, executing such tests at Mach 10 avoids some known concerns and will aid in solving new problems. XSWBLI are a highly unsteady phenomena and the generation of XSWBLI at lower Mach numbers can prove to be a significant challenge. This concern will be somewhat mitigated in the Mach 10 flow, as boundary layers become increasingly stabilized, but some difficulty in achieving transition is still expected. Modelling SWBLI in the presence of transitional and turbulent boundary layers has also proven to be difficult, so a high-Mach number experiment which applies non-intrusive and optical diagnostics will aid in solving a unique problem as well as advancing the understanding and characterization of an aerodynamic surface at Mach 10.The NASA LaRC 31-inch Wind Tunnel incorporates a test section having a cross-section of 31-inches × 31-inches and provides optical access to the test section via three (3) ultra-violet (UV) transmitting windows on the top, side, and bottom. The Mach 10 operating conditions will consist of pressures (P0) ranging from 2.4 to 10MPa (348 to 1,450 psi) at a temperature (T0) of 1,000 K (1,800 °R). The NASA LaRC 31-inch wind tunnel will deliver 1-minute blow-down runs, of which 30-45 seconds will be consumed to reach the aforementioned test conditions. The pump down time between runs will be approximately 45-60 minutes, which will provide for 6-10 test runs per day over the course of a weeklong entry. The proposed flat plate model will be constructed of stainless steel with geometry consisting of a10-inch × 30-inch upper surface and a 2-inch thickness. The model will be designed to support multiple leading-edge inserts in order to examine blunt, round, and sharp leading edges at Mach 10. Adjustments will be made to manage boundary layer thickness as well as the strength and size of the shock interaction region for each test. Measurements and diagnostics will be performed though high-speed Schlieren, on-body high-speed pressure transducers, IR thermography, and oil flow visualization. Hypersonic vehicle applications have and will continue to emerge at the forefront of aerospace. The NASA-UTSA-UTSI team realizes the value of characterizing SWBLI, XSWBLI, and SWTBLI behaviors well beyond single-digit hypersonic Mach numbers. As hypersonic vehicle speed capabilities continue to increase, measurement and diagnostic methods for Mach numbers of 10 and beyond will provide the foundation for a firm understanding of flow field behavior which will directly influence the advancement of technologies towards the design and manufacturing of high-speed aerodynamic surfaces, controls, thermal protection systems, acoustic treatments, and structural components. The use of non-intrusive and optical diagnostic methods in such experimentation is pivotal in developing the visualization and empirical data necessary to advance the aforementioned technology areas.

Shockwave/Boundary-Layer Interactions↗

DOE OSTI2023

Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding

Abstract Motivation The vast expansion of sequence data generated from single organisms and microbiomes has precipitated the need for faster and more sensitive methods to assess evolutionary and functional relationships between proteins. Representing proteins as sets of short peptide sequences (kmers) has been used for rapid, accurate classification of proteins into functional categories; however, this approach employs an exact-match methodology and thus may be limited in terms of sensitivity and coverage. We have previously used similarity groupings, based on the chemical properties of amino acids, to form reduced character sets and recode proteins. This amino acid recoding (AAR) approach simplifies the construction of protein representations in the form of kmer vectors, which can link sequences with distant sequence similarity and provide accurate classification of problematic protein families. Results Here, we describe Snekmer, a software tool for recoding proteins into AAR kmer vectors and performing either (i) construction of supervised classification models trained on input protein families or (ii) clustering for de novo determination of protein families. We provide examples of the operation of the tool against a set of nitrogen cycling families originally collected using both standard hidden Markov models and a larger set of proteins from Uniprot and demonstrate that our method accurately differentiates these sequences in both operation modes. Availability and implementation Snekmer is written in Python using Snakemake. Code and data used in this article, along with tutorial notebooks, are available at http://github.com/PNNL-CompBio/Snekmer under an open-source BSD-3 license. Supplementary information Supplementary data are available at Bioinformatics Advances online.

59 BASIC BIOLOGICAL SCIENCES↗