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At least 1,639 records · Page 91

Particulate Emission and Optical Measurements in n-Heptane Low-Swirl Non-Premixed Flames at Elevated Pressures

A series of ground combustion tests conducted at elevated pressures demonstrates in-chamber optical measurements of soot emissions, combined with conventional gaseous and particle emissions sampling techniques. Utilizing a micro-radial-entry counter-swirl (MRX) burner, we successfully stabilized an n-heptane low-swirl, non-premixed spray flame across a wide range of equivalence ratios at pressures reaching 250 psia. Our optical diagnostics feature a temporally gated diffused-backlight illumination extinction imaging (DBI-EI) system, equipped with a 470-nm strobe high-intensity LED array as the illumination source, along with a line-of-sight telecentric camera. By accessing the flame tube, the pulsed DBI-EI provides illuminating optical extinction images, enabling experimental estimation of soot volume fractions within the reaction zone. This imaging technique will allow for real-time observation of soot formation dynamics occurring above the air-blast fuel injector. To further enhance our analysis, we employed simultaneous gaseous and particulate extractive diagnostics, interpreting in-flame particulate information through CO2 sampling, exhaust particle sizing, and particle counting. The processed dataset reveals a promising application of DBI-EI for propulsion emission analysis in high-pressure environments, where optical beam-steering effects can significantly impact results. This report is essential to bridging the divide between in-flame optical diagnostics and exhaust extractive measurements. By achieving an understanding of non-premixed combustion emission characteristics, we attempt to provide invaluable data for computer code validation, advancing the field of combustion research and supporting the development of cleaner, more efficient engines.

high-pressure flame↗

Particulate Emission and Optical Measurements in n-Heptane Low-Swirl Non-Premixed Flames at Elevated Pressures

A series of ground combustion tests conducted at elevated pressures demonstrates in-chamber optical measurements of soot emissions, combined with conventional gaseous and particle emissions sampling techniques. Utilizing a micro-radial-entry counter-swirl (MRX) burner, we successfully stabilized an n-heptane low-swirl, non-premixed spray flame across a wide range of equivalence ratios at pressures reaching 250 psia. Our optical diagnostics feature a temporally gated diffused-backlight illumination extinction imaging (DBI-EI) system, equipped with a 470-nm strobe high-intensity LED array as the illumination source, along with a line-of-sight telecentric camera. By accessing the flame tube, the pulsed DBI-EI provides illuminating optical extinction images, enabling experimental estimation of soot volume fractions within the reaction zone. This imaging technique will allow for real-time observation of soot formation dynamics occurring above the air-blast fuel injector. To further enhance our analysis, we employed simultaneous gaseous and particulate extractive diagnostics, interpreting in-flame particulate information through CO2 sampling, exhaust particle sizing, and particle counting. The processed dataset reveals a promising application of DBI-EI for propulsion emission analysis in high-pressure environments, where optical beam-steering effects can significantly impact results. This report is essential to bridging the divide between in-flame optical diagnostics and exhaust extractive measurements. By achieving an understanding of non-premixed combustion emission characteristics, we attempt to provide invaluable data for computer code validation, advancing the field of combustion research and supporting the development of cleaner, more efficient engines.

high-pressure flame↗

Does the International Space Station Leak DNA? Preliminary Results from the ISS External Microorganisms Payload

Existing crewed spacecraft like the ISS (International Space Station) leak by design. The ISS routinely releases gas to maintain life support systems and when astronauts exit the station to perform space walks. The chemical component of this leakage is well characterized, but the biological components are not. The ISS is not subject to planetary protection requirements, but planned missions to Mars will use similar systems and will be subject to planetary protection requirements. If detectable microorganisms are escaping through vents and or airlocks we may need to redesign our crewed habitats to minimize this type of contamination. To test the hypothesis that microorganisms from inside ISS are detectable on exterior surfaces an astronaut used the ISS External Microorganisms sampling kit (Rucker et al. 2018) to sample exterior surfaces of the ISS during an EVA (Extra Vehicular Activity) in January of 2025. These samples were returned to Earth for DNA extraction and sequencing. We successfully, extracted and sequenced bacterial, fungal and viral DNA from these samples that was not present in the negative controls. These results should help NASA refine the planetary protection requirements for crewed missions. Methods: The samples were collected using sterile, DNA free, buccal swabs (23 mm. diameter) housed in custom canisters. Each canister uses a 0.2 μm Teflon filter to maintain sterility as the caddy, holding 8 swabs moves in and out of vacuum. The astronaut sampled the: 1) airlock vestibule, 2) airlock thermal cover, 3) a gap in the micrometeorite shielding near the airlock, 4) a handrail near the airlock, 5) the Carbon Dioxide Removal Assembly vent, and 6) the Vacuum Exhaust System vent. The seventh swab was exposed to vacuum during the EVA without touching it to a surface. The eighth swab, a negative control, was not opened until the caddy returned to Earth. DNA was extracted from the swabs using a QIamp UCP Pathogen kit and prepared for sequencing on an Aviti (Element Biosciences) sequencer (Arslan et al. 2024). The resulting sequences were analyzed using the EDGE Bioinformatics platform (Li et al. 2017). The sequences were analyzed individually using tools like BLAST, GOTTCHA2, Kraken2, and PanGIA. The data were also assembled into metagenome assembled genomes) using tools like CONCOCT, MaxBin2 and MetaBAT2. Results: We successfully extracted and sequenced bacterial, archaeal, fungal and viral DNA from all seven samples. The handrail swab had the lowest number of reads (768,651) and the airlock thermal cover had the highest number of reads (8,819,230). These samples contain DNA from human associated bacteria (e.g. Crynebacterium riegelii ), fungi (.e.g. Penicillium rubens ), and viruses (e.g Alphapapillomavirus ). Conclusion: Preliminary interpretation suggest that the airlock and the space suits themselves are the largest sources of contaminant DNA. Most if not all of the DNA is from organisms known to be present inside the ISS. Vents attached to life support systems may be a lesser source of biological contamination. Further analysis should help NASA address planetary protection knowledge gaps for crewed missions.

Aaron B Regberg↗

The Combined Finite-Discrete Element Method applied to the Study of Rock Fracturing Behavior in 3D

Since its introduction the combined finite-discrete element method (FEM/DEM), has become an excellent tool to address a wide range of problems involving fracturing and fragmentation of solids. Within the context of rock mechanics, the FEM/DEM method has been applied to many complex industrial problems such as block caving, deep mining techniques, rock blasting, seismic waves, packing problems, rock crushing problems, etc. In the real world most of the problems involving fracture and fragmentation of solids are three dimensional problems. With the aim of addressing these problems an improved 2D/3D FEM/DEM capability has been developed at Los Alamos National Laboratory (LANL). These capabilities include state of the art 3D contact detection, contact interaction, constitutive material models, and fracture models. In this paper, Split Hopkinson Pressure Bar (SHPB) Brazilian experiments are simulated using this improved 2D/3D FEM/DEM approach which is implemented in LANL's MUNROU (Munjiza-Rougier) code. The results presented in this work show excellent agreement with both the SHPB experiments and previous 2D numerical simulations performed by other FEM/DEM research groups.

CALCULATION METHODS↗

Building an Efficient Model for Afterburn Energy Release

Many explosives will release additional energy after detonation as the detonation products mix with the ambient environment. This additional energy release, referred to as afterburn, is due to combustion of undetonated fuel with ambient oxygen. While the detonation energy release occurs on a time scale of microseconds, the afterburn energy release occurs on a time scale of milliseconds with a potentially varying energy release rate depending upon the local temperature and pressure. This afterburn energy release is not accounted for in typical equations of state, such as the Jones-Wilkins-Lee (JWL) model, used for modeling the detonation of explosives. Here we construct a straightforward and efficient approach, based on experiments and theory, to account for this additional energy release in a way that is tractable for large finite element fluid-structure problems. Barometric calorimeter experiments have been executed in both nitrogen and air environments to investigate the characteristics of afterburn for C-4 and other materials. These tests, which provide pressure time histories, along with theoretical and analytical solutions provide an engineering basis for modeling afterburn with numerical hydrocodes. It is toward this end that we have constructed a modified JWL equation of state to account for afterburn effects on the response of structures to blast. The modified equation of state includes a two phase afterburn energy release to represent variations in the energy release rate and an afterburn energy cutoff to account for partial reaction of the undetonated fuel.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Towards mitigating explosive threats using quantum controlled initiation

Quantum control of localized energy deposition into an energetic material is being investigated as a method to allow controlled initiation and propagation of action without transition to detonation. Quantum controlled initiation (QCI) of explosives utilize time dependent phase shaped ultraviolet (UV) electric fields to drive the energetic chemical systems towards reaction. QCI searches for an optimally shaped ultrafast laser pulse that will guide energy flow along a desired path. QCI can be exploited as a stand-off mitigation technology that strives to reduce the impact of explosive blasts on people and property by initiating controlled low order reaction. Quantum controlled initiation experiments require: (1) optimally shaped light pulses, (2) pulse shaping measurement, (3) feedback control algorithms, and (4) feedback measurement methods. Femtosecond laser pulse shaping in the UV at 400 nm employs a fused silica acousto-optic modulator (AOM) pulse shaper that consists of a 4-f zero dispersion compressor. Tr sient absorption spectroscopy is used to measure the pulse shaper effects. Both global and local optimization search routines such as genetic algorithm, differential evolution, and downhill simplex are used to search for the optimal pulse shape. Hexanitroazobenzene (HNAB), Trinitroanaline (TNA) and Diaminoazozyfurazan (DAAF) are excited to the first electronic state with 400 nm light. Our initiation experiments are studying the effect of phase shaped 400 nm pulses on HNAB, TNA and DAAF. The transient absorption spectra for each material have been obtained and note worthy regions further investigated with single parameter control (second order spectral phase and energy). Many systems have simple intensity control such as that shown by DAAF. TNA and HNAB have spectral features that are not single parameter driven and are being further investigated to obtain fully optimized complex control.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

A general higher-order remap algorithm for ALE calculations

A numerical technique for solving the equations of fluid dynamics with arbitrary mesh motion is presented. The three phases of the Arbitrary Lagrangian Eulerian (ALE) methodology are outlined: the Lagrangian phase, grid relaxation phase and remap phase. The Lagrangian phase follows a well known approach from the HEMP code; in addition the strain rate andflow divergence are calculated in a consistent manner according to Margolin. A donor cell method from the SALE code forms the basis of the remap step, but unlike SALE a higher order correction based on monotone gradients is also added to the remap. Four test problems were explored to evaluate the fidelity of these numerical techniques, as implemented in a simple test code, written in the C programming language, called Cercion. Novel cell-centered data structures are used in Cercion to reduce the complexity of the programming and maximize the efficiency of memory usage. The locations of the shock and contact discontinuity in the Riemann shock tube problem are well captured. Cercion demonstrates a high degree of symmetry when calculating the Sedov blast wave solution, with a peak density at the shock front that is similar to the value determined by the RAGE code. For a flyer plate test problem both Cercion and FLAG give virtually the same velocity temporal profile at the target-vacuum interface. When calculating a cylindrical implosion of a steel shell, Cercion and FLAG agree well and the Cercion results are insensitive to the use of ALE.

36 MATERIALS SCIENCE↗

A LANL Scientist's Dream Takes Off to Zap Rocks on Mars

Roger Wiens, with a team of 40 people at Los Alamos National Laboratory and the collaboration of the French space institute IRAP, created ChemCam, a laser spectrometer and telescope device aboard the Curiosity rover. ChemCam will blast rocks from as far as 7 meters, vaporize bits of their surfaces, and spectroscopically determine their chemical composition, aiding in the search for life on Mars, and making this scientist's boyhood dream a reality.

42 ENGINEERING↗

The Effects of Heterogeneities on Seismic Wave Propagation in the Climax Stock

The Comprehensive Nuclear Test-Ban Treaty requires the ability to detect low-yield (less than 150kton) nuclear events. This kind of monitoring can only be done seismically on a regional scale (within 2000km). At this level, it is difficult to distinguish between low-yield nuclear events and non-nuclear events of similar magnitude. In order to confidently identify a nuclear event, a more detailed understanding of nuclear seismic sources is needed. In particular, it is important to know the effects of local geology on the seismic signal. This study focuses on P-wave velocity in heterogeneous granitoid. The Source Physics Experiment (SPE) is currently performing low-yield tests with chemical explosives at the Nevada National Security Site (NNSS). The exact test site was chosen to be in the Climax Stock, a cretaceous granodiorite and quartz-monzonite pluton located in Area 15 of the NNSS. It has been used in the past for the Hard Hat and Pile Driver nuclear tests, which provided legacy data that can be used to simulate wave propagation. The Climax Stock was originally chosen as the site of the SPE partly because of its assumed homogeneity. It has since been discovered that the area of the stock where the SPE tests are being performed contains a perched water table. In addition, the stock is known to contain an extensive network of faults, joints, and fractures, but the exact effect of these structural features on seismic wave velocity is not fully understood. The SPE tests are designed to seismically capture the explosion phenomena from the near- to the far-field transition of the seismic waveform. In the first SPE experiment, 100kg of chemical explosives were set off at a depth of 55m. The blast was recorded with an array of sensors and diagnostics, including accelerometers, geophones, rotational sensors, short-period and broadband seismic sensors, Continuous Reflectometry for Radius vs. Time Experiment, Time of Arrival, Velocity of Detonation, and infrasound sensors. The focus of this study is two-fold: (1) the geophone array that was focused over the SPE shot and (2) a high-resolution seismic profile that was recently acquired at the field site. The geophone array was placed radially around the SPE shot in five directions with 100m spacing and out to a distance of 2 km. The high-resolution profile was about 475m in length with station and shot spacing of 5m using a 7000lb mini-vibe as a source. In both data sets, the first arrivals will be used to develop velocity models. For the geophone array, 1-D P-wave velocity models will be developed to determine an average apparent velocity of the Climax Stock. The high-resolution data will be used to develop a 2-D P-wave velocity model along the seismic profile. This is in an effort to elucidate the water table in more detail and provide additional information on the near-surface structure. These results will be used in the overall modeling effort to fully characterize the test bed and develop a physics-based model to simulate seismic energy from the SPE events.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Surface modification to prevent oxide scale spallation

A surface modification to prevent oxide scale spallation is disclosed. The surface modification includes a ferritic stainless steel substrate having a modified surface. A cross-section of the modified surface exhibits a periodic morphology. The periodic morphology does not exceed a critical buckling length, which is equivalent to the length of a wave attribute observed in the cross section periodic morphology. The modified surface can be created using at least one of the following processes: shot peening, surface blasting and surface grinding. A coating can be applied to the modified surface.

36 MATERIALS SCIENCE↗

Novel Visual and Analytical Methods in Repurposing Legacy Scientific Code - A Case Study

Scientific computing is dominated by team-authored legacy code that has evolved over decades with the purpose of capturing the evolving understanding of a scientific discipline. Accumulated deprecated code, various optimization techniques, and evolving algorithms lead to convoluted source code that is impractical to reverse engineer using mainstream methods. This prevents codes from being truly repeatable or understandable, which are two of the most essential needs in scientific computing. We refactored a long-standing implementation of a common biosequence alignment algorithm in an effort to reproduce its salient behaviors in usable form. Because of the sheer size and complexity of this code base, we developed custom tools to visualize and manipulate the source code behavior under a variety of conditions. We present a case study of extracting and refactoring the algorithmic core and a novel process of discovery/prototyping/testing using a combination of openly available and custom-built tools. The result is a reduction in code size of over 2 orders of magnitude while reconstructing the key protein alignment function in BLAST

bioinformatics, scientific computing↗

Domain-Specific Languages For Developing and Deploying Signature Discovery Workflows

Domain-agnostic Signature Discovery entails scientific investigation across multiple domains through the re-use of existing algorithms into workflows. The existing algorithms may be written in any programming language for various hardware architectures (e.g., desktops, commodity clusters, and specialized parallel hardware platforms). This raises an engineering issue in generating Web services for heterogeneous algorithms so that they can be composed into a scientific workflow environment (e.g., Taverna). In this paper, we present our software tool that defines two simple Domain-Specific Languages (DSLs) to automate these processes: SDL and WDL. Our Service Description Language (SDL) describes key elements of a signature discovery algorithm and generates the service code. The Workflow Description Language (WDL) describes the pipeline of services and generates deployable artifacts for the Taverna workflow management system. We demonstrate our tool with a landscape classification example that is represented by BLAST workflows composed of services that wrap original scripts.

Jacob, Ferosh↗

Site Characterization of the Source Physics Experiment Phase II Location Using Seismic Reflection Data

An objective of the Source Physics Experiment (SPE) is to identify low-yield nuclear explosions from a regional distance. Low-yield nuclear explosions can often be difficult to discriminate among the clutter of natural and man-made explosive events (e.g., earthquakes and mine blasts). The SPE is broken into three phases. Phase I has provided the first of the physics-based data to test the empirical models that have been used to discriminate nuclear events. The Phase I series of tests were placed within a highly fractured granite body. The evolution of the project has led to development of Phase II, to be placed within the opposite end member of geology, an alluvium environment, thereby increasing the database of waveforms to build upon in the discrimination models. Both the granite and alluvium sites have hosted nearby nuclear tests, which provide comparisons for the chemical test data. Phase III of the SPE is yet to be determined.

Seismic↗

Sintered silver joints via controlled topography of electronic packaging subcomponents

Disclosed are sintered silver bonded electronic package subcomponents and methods for making the same. Embodiments of the sintered silver bonded EPSs include topography modification of one or more metal surfaces of semiconductor devices bonded together by the sintered silver joint. The sintered silver bonded EPSs include a first semiconductor device having a first metal surface, the first metal surface having a modified topography that has been chemically etched, grit blasted, uniaxial ground and/or grid sliced connected to a second semiconductor device which may also include a first metal surface with a modified topography, a silver plating layer on the first metal surface of the first semiconductor device and a silver plating layer on the first metal surface of the second semiconductor device and a sintered silver joint between the silver plating layers of the first and second semiconductor devices which bonds the first semiconductor device to the second semiconductor device.

36 MATERIALS SCIENCE↗

Suppressors made from intermetallic materials

Disclosed are several examples of apparatuses for suppressing the blast and flash produced as a projectile is expelled by gases from a firearm. In some examples, gases are diverted away from the central chamber to an expansion chamber by baffles. The gases are absorbed by the expansion chamber and desorbed slowly, thus decreasing pressure and increasing residence time of the gases. In other examples, the gases impinge against a plurality of rods before expanding through passages between the rods to decrease the pressure and increase the residence time of the gases. These and other exemplary suppressors are made from an intermetallic material composition for enhanced strength and oxidation resistance at high operational temperatures.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Materials for Advanced Ultrasupercritical Steam Turbines Task 4: Cast Superalloy Development

The Steam Turbine critical stationary structural components are high integrity Large Shell and Valve Casing heavy section Castings, containing high temperature steam under high pressures. Hence to support the development of advanced materials technology for use in an AUSC steam turbine capable of operating with steam conditions of 760°C (1400°F) and 35 Mpa (5000 psia), Casting alloy selection and evaluation of mechanical, metallurgical properties and castability with robust manufacturing methods are mandated. Alloy down select from Phase 1 based on producability criteria and creep rupture properties tested by NETL-Albany and ORNL directed the consortium to investigate cast properties of Haynes 282 and Haynes 263. The goals of Task 4 in Phase 2 are to understand a broader range of mechanical properties, the impact of manufacturing variables on those properties. Scale up the size of heats to production levels to facilitate the understanding of the impact of heat and component weight, on metallurgical and mechanical behavior. GE Power & Water Materials and Processes Engineering for the Phase 2, Task 4.0 Castings work, systematically designed and executed casting material property evaluation, multiple test programs. Starting from 15 lbs. cylinder castings to world’s first 17,000 lbs. poured weight, heavy section large steam turbine partial valve Haynes 282 super alloy casting. This has demonstrated scalability of the material for steam Turbine applications. Activities under Task 4.0, Investigated and characterized various mechanical properties of Cast Haynes 282 and Cast Nimonic 263. The development stages involved were: 1) Small Cast Evaluation: 4 inch diam. Haynes 282 and Nimonic 263 Cylinders. This provided effects of liquidus super heat range and first baseline mechanical data on cast versions of conventional vacuum re-melted and forged Ni based super alloys. 2) Step block castings of 300 lbs. and 600 lbs. Haynes 282 from 2 foundry heats were evaluated which demonstrated the importance of proper heat treat cycles for Homogenization, and Solutionizing parameters selection and implementation. 3) Step blocks casting of Nimonic 263: Carried out casting solidification simulation analysis, NDT inspection methods evaluation, detailed test matrix for Chemical, Tensile, LCF, stress rupture, CVN impact, hardness and J1C Fracture toughness section sensitivity data and were reported. 4) Centrifugal Casting of Haynes 282, weighing 1400 lbs. with hybrid mold (half Graphite and half Chromite sand) mold assembly was cast using compressor casing production tooling. This test provided Mold cooling rates influence on centrifugally cast microstructure and mechanical properties. Graphite mold section out performs sand mold across all temperatures for 0.2% YS; %Elongation, %RA, UTS at 1400°F. Both Stress-LMP and conditional Fracture toughness plots data were in the scatter band of the wrought alloy. 5) Fundamental Studies on Cooling rates and SDAS test program. Evaluated the influence of 6 mold materials Silica, Chromite, Alumina, Silica with Indirect Chills, Zircon and Graphite on casting solidification cooling rates. Actual Casting cooling rates through Liquidus to Solidus phase transition were measured with 3 different locations based thermocouples placed in each mold. Compared with solidification simulation cooling rates and measurement of SDAS, microstructure features were reported. The test results provided engineered casting potential methods, applicable for heavy section Haynes 282 castings for optimal properties, with foundry process methods and tools. 6) Large casting of Haynes 282 Drawings and Engineering FEM models and supplemental requirements with applicable specifications were provided to suppliers for the steam turbine proto type feature valve casing casting. Molding, melting and casting pouring completed per approved Manufacturing Process Plan during 2014 Q4. The partial valve casing was successfully cast after casting methods were validated with solidification simulation analysis and the casting met NDT inspection and acceptance criteria. Heat treated and sectioned to extract trepan samples at different locations comparing with cast on coupons test data. Material properties requisite for design, such as tensile, creep/rupture, LCF, Fracture Toughness, Charpy V-notch chemical analysis testing were carried out. The test results will be presented in the final report. The typical Haynes 282 large size Steam Turbine production casting from Order to Delivery foundry schedule with the activity break up is shown in Figures 107 and 108. • From Purchase Order placement to Casting pouring ~ 26 weeks. 1. Sales and commercial review 3 2. Engineering Drawings/models review 4 3. Pattern and core box manufacturing 6 4. Casting process engineering review 4 5. FEM and solidification simulation analysis 4 6. Gating & Feeder Attachments, Ceramic tiling 2 7. Molding and coremaking production scheduling 6 8. Melting planning and schedule 3 9. Pouring, cooling and shake out 2 • From Pouring to casting Delivery ~ 29 weeks 10. Shot blast and riser cutting, gates removal 3 11. Homogenizing , solutionizing HT furnace prep 4 12. Grinding, Fettling 2 13. Aging HT Cycle, cooling 2 14. VT and LPT NDT inspections 2 15. Radiographic inspection 4 16. Mechanical testing, Chemical analysis test certs 4 17. Casting weld repair upgrades and Aging PWHT 4 18. NDT after weld repairs and casting upgrades 3 19. Casting Final Inspection and test certifications 3 20. Package and delivery 2 Hence the Total Lead time from P.O to Casting delivery is approximately 55 weeks. The Task 4.2 and Task 4.3 activities and reporting completed.

Thangirala, Mani↗

Compare Gene Profiles

Compare Gene Profiles (CGP) performs pairwise gene content comparisons among a relatively large set of related bacterial genomes. CGP performs pairwise BLAST among gene calls from a set of input genome and associated annotation files, and combines the results to generate lists of common genes, unique genes, homologs, and genes from each genome that differ substantially in length from corresponding genes in the other genomes. CGP is implemented in Python and runs in a Linux environment in serial or parallel mode.

Source record↗

j5 v2.8.4

j5 automates and optimizes the design of the molecular biological process of cloning/constructing DNA. j5 enables users to benefit from (combinatorial) multi-part scar-less SLIC, Gibson, CPEC, Golden Gate assembly, or variants thereof, for which automation software does not currently exist, without the intense labor currently associated with the process. j5 inputs a list of the DNA sequences to be assembled, along with a Genbank, FASTA, jbei-seq, or SBOL v1.1 format sequence file for each DNA source. Given the list of DNA sequences to be assembled, j5 first determines the cost-minimizing assembly strategy for each part (direct synthesis, PCR/SOE, or oligo-embedding), designs DNA oligos with Primer3, adds flanking homology sequences (SLIC, Gibson, and CPEC; optimized with Primer3 for CPEC) or optimized overhang sequences (Golden Gate) to the oligos and direct synthesis pieces, and utilizes BLAST to check against oligo mis-priming and assembly piece incompatibility events. After identifying DNA oligos that are already contained within a local collection for reuse, the program estimates the total cost of direct synthesis and new oligos to be ordered. In the instance that j5 identifies putative assembly piece incompatibilities (multiple pieces with high flanking sequence homology), the program suggests hierarchical subassemblies where possible. The program outputs a comma-separated value (CSV) file, viewable via Excel or other spreadsheet software, that contains assembly design information (such as the PCR/SOE reactions to perform, their anticipated sizes and sequences, etc.) as well as a properly annotated genbank file containing the sequence resulting from the assembly, and appends the local oligo library with the oligos to be ordered j5 condenses multiple independent assembly projects into 96-well format for high-throughput liquid-handling robotics platforms, and generates configuration files for the PR-PR biology-friendly robot programming language. j5 thus provides a new way to design DNA assembly procedures much more productively and efficiently, not only in terms of time, but also in terms of cost. To a large extent, however, j5 does not allow people to do something that could not be done before by hand given enough time and effort. An exception to this is that, since the very act of using j5 to design the DNA assembly process standardizes the experimental details and workflow, j5 enables a single person to concurrently perform the independent DNA construction tasks of an entire group of researchers. Currently, this is not readily possible, since separate researchers employ disparate design strategies and workflows, and furthermore, their designs and workflows are very infrequently fully captured in an electronic format which is conducive to automation.

Hillson, Nathan↗