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At least 667 records · Page 37

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DOE OSTI2020

Comparison of modular analytical wake models to the Lillgrund wind plant

Efficient and accurate wake models are required for wind plant performance modeling and the suite of engineering processes that support wind plant layout, control, and monitoring. Although many analytical and engineering wake models with low computational costs have been proposed, their ability to represent the power production of large wind plants in a wide range of atmospheric conditions is not completely understood. The following validation study reviews the underlying theory for analytical wake models, outlines quality control procedures for observational data, and compares model results with observational data from the Lillgrund Wind Plant. Lillgrund makes a valuable case study for wake modeling because of its regular arrangement and the relatively close spacing of constituent wind turbines, which lead to regular and significant wake interactions within the wind plant and the development of deep array flow conditions. Formulations for the velocity deficit, wake-added turbulence, and wake superposition methods are considered in a modular sense, yielding many possible configurations to represent wind turbine wakes, of which seven are examined in detail. Velocity deficit models that account for flow conditions in the near wake are better able to reproduce power production for wind turbines in the transitional region of the wind plant, where wind turbines experience as many as five wakes from upstream turbines. Finally, in the deep array, where power production reaches asymptotic values and wake statistics become quasi-periodic, wake superposition schemes become the largest driver in error reduction; using the linear or maximum wake superposition methods can reduce the relative root mean square error by as much as 40% in the deep array.

17 WIND ENERGY↗

DOE OSTI2024

Ion trap with in-vacuum high numerical aperture imaging for a dual-species modular quantum computer

Photonic interconnects between quantum systems will play a central role in both scalable quantum computing and quantum networking. Entanglement of remote qubits via photons has been demonstrated in many platforms; however, improving the rate of entanglement generation will be instrumental for integrating photonic links into modular quantum computers. We present an ion trap system that has the highest reported free-space photon collection efficiency for quantum networking. We use a pair of in-vacuum aspheric lenses, each with a numerical aperture of 0.8, to couple 10(1)% of the 493 nm photons emitted from a 138Ba+ ion into single-mode fibers. We also demonstrate that proximal effects of the lenses on the ion position and motion can be mitigated.

Instruments & Instrumentation↗

DOE OSTI2024

DL_POLY Quantum 2.0: A modular general-purpose software for advanced path integral simulations

DL_POLY Quantum 2.0, a vastly expanded software based on DL_POLY Classic 1.10, is a highly parallelized computational suite written in FORTRAN77 with a modular structure for incorporating nuclear quantum effects into large-scale/long-time molecular dynamics simulations. This is achieved by presenting users with a wide selection of state-of-the-art dynamics methods that utilize the isomorphism between a classical ring polymer and Feynman’s path integral formalism of quantum mechanics. Here, the flexible and user-friendly input/output handling system allows the control of methodology, integration schemes, and thermostatting. DL_POLY Quantum is equipped with a module specifically assigned for calculating correlation functions and printing out the values for sought-after quantities, such as dipole moments and center-of-mass velocities, with packaged tools for calculating infrared absorption spectra and diffusion coefficients.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Cryogen-free modular scanning tunneling microscope operating at 4-K in high magnetic field on a compact ultra-high vacuum platform

One of the daunting challenges in modern low temperature scanning tunneling microscopy (STM) is the difficulty of combining atomic resolution with cryogen-free cooling. Further functionality needs, such as ultra-high vacuum (UHV), high magnetic field (HF), and compatibility with μm-sized samples, pose additional challenges to an already ambitious build. We present the design, construction, and performance of a cryogen-free, UHV, low temperature, and high magnetic field system for modular STM operation. An internal vibration isolator reduces vibrations in this system, allowing for atomic resolution STM imaging while maintaining a low base temperature of ∼4 K and magnetic fields up to 9 T. Samples and tips can be conditioned in situ utilizing a heating stage, an ion sputtering gun, an e-beam evaporator, a tip treater, and sample exfoliation. In situ sample and tip exchange and alignment are performed in a connected UHV room temperature stage with optical access. Multisite operation without breaking vacuum is enabled by a unique quick-connect STM head design. A novel low-profile vertical transfer mechanism permits transferring the STM between room temperature and the low temperature cryostat.

Instruments & Instrumentation↗

DOE OSTI2018

Human N -acetylglucosaminyltransferase II substrate recognition uses a modular architecture that includes a convergent exosite

Asn-linked oligosaccharides are extensively modified during transit through the secretory pathway, first by trimming of the nascent glycan chains and subsequently by initiating and extending multiple oligosaccharide branches from the trimannosyl glycan core. Trimming and branching pathway steps are highly ordered and hierarchal based on the precise substrate specificities of the individual biosynthetic enzymes. A key committed step in the synthesis of complex-type glycans is catalyzed by N-acetylglucosaminyltransferase II (MGAT2), an enzyme that generates the second GlcNAcβ1,2- branch from the trimannosyl glycan core using UDP-GlcNAc as the sugar donor. We determined the structure of human MGAT2 as a Mn 2+ -UDP donor analog complex and as a GlcNAcMan 3 GlcNAc 2 -Asn acceptor complex to reveal the structural basis for substrate recognition and catalysis. The enzyme exhibits a GT-A Rossmann-like fold that employs conserved divalent cation-dependent substrate interactions with the UDP-GlcNAc donor. MGAT2 interactions with the extended glycan acceptor are distinct from other related glycosyltransferases. These interactions are composed of a catalytic subsite that binds the Man-α1,6- monosaccharide acceptor and a distal exosite pocket that binds the GlcNAc-β1,2Man-α1,3Manβ- substrate “recognition arm.” Recognition arm interactions are similar to the enzyme–substrate interactions for Golgi α-mannosidase II, a glycoside hydrolase that acts just before MGAT2 in the Asn-linked glycan biosynthetic pathway. Here, these data suggest that substrate binding by MGAT2 employs both conserved and convergent catalytic subsite modules to provide substrate selectivity and catalysis. More broadly, the MGAT2 active-site architecture demonstrates how glycosyltransferases create complementary modular templates for regiospecific extension of glycan structures in mammalian cells.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity

Relating the macroscopic properties of protein-based materials to their underlying component microstructure is an outstanding challenge. Here, we exploit computational design to specify the size, flexibility, and valency of de novo protein building blocks, as well as the interaction dynamics between them, to investigate how molecular parameters govern the macroscopic viscoelasticity of the resultant protein hydrogels. We construct gel systems from pairs of symmetric protein homo-oligomers, each comprising 2, 5, 24, or 120 individual protein components, that are crosslinked either physically or covalently into idealized step-growth biopolymer networks. Through rheological assessment, we find that the covalent linkage of multifunctional precursors yields hydrogels whose viscoelasticity depends on the crosslink length between the constituent building blocks. In contrast, reversibly crosslinking the homo-oligomeric components with a computationally designed heterodimer results in viscoelastic biomaterials exhibiting fluid-like properties under rest and low shear, but solid-like behavior at higher frequencies. Exploiting the unique genetic encodability of these materials, we demonstrate the assembly of protein networks within living mammalian cells and show via fluorescence recovery after photobleaching (FRAP) that mechanical properties can be tuned intracellularly in a manner similar to formulations formed extracellularly. We anticipate that the ability to modularly construct and systematically program the viscoelastic properties of designer protein-based materials could have broad utility in biomedicine, with applications in tissue engineering, therapeutic delivery, and synthetic biology.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Large-scale Multiphysics Simulations of Small Modular Reactors Operating in Natural Circulation

Thanks to the advancements in high-performance computing, advanced modeling and simulation have become crucial in driving the development and deployment of next-generation nuclear reactors, such as small modular reactors (SMRs). SMRs offer the promise of cost-effective baseload electricity production and improved safety, while addressing some of the challenges associated with large reactor designs, such as high capital costs and extended construction timelines. As part of the Exascale Computing Project, the large-scale multiphysics simulation of an entire SMR primary system has been achieved by combining computational fluid dynamics and neutronics. In addition to the successful demonstration of full-core SMR simulations, the current study integrated the impact of natural circulation into the system. Natural circulation is the primary mechanism driving coolant circulation in SMRs. The mass flow rate in the core depends on the core power, and a numerical model has been developed to predict it. The pressure drop caused by the helical coil steam generator was also accounted for by developing a pressure drop correlation based on high-fidelity large eddy simulation results, further improving prediction accuracy. In conclusion, the results of the study demonstrate that the implemented natural circulation model is effective in predicting the responses of SMR full-core multiphysics simulations.

ECP↗

DOE OSTI2025

Accelerated Fuel Qualification of Fast Modular Reactor Fuel in a Thermal Reactor: Modeling and Simulation Paired with Irradiation Testing

The accelerated fuel qualification (AFQ) methodology is applied by simulating accelerated fuel tests of the General Atomics Electromagnetic Systems’ fuel system for its 44-MW(electric) gas-cooled, fast-spectrum fast modular reactor (FMR). This fuel is comprised of UO 2 pellets in SiGA® cladding, a silicon carbide ceramic matrix composite. Fast reactors, like the FMR, offer many benefits, including high fuel utilization and flexibility, but may require a lengthy material design process if tests are performed using fast neutron irradiation alone. A thermal neutron irradiation can instead be used to rapidly test how well key components of the current material models extend to high burnup. Thermal neutrons produce a different radial power distribution within the pin than fast neutrons. However, the temperature and burnup values for the two neutron types are comparable, and the differences between the simulated fuel responses are relatively small, demonstrating the weak sensitivity of the physics-based fuel model calculations on the neutron type and the irradiation rate. Furthermore, the deformation of the SiGA cladding saturates after about 1 displacement per atom for both neutron spectra. In an accelerated fuel test, the irradiation time required to reach the target fuel burnup can be reduced by a factor of 3 by using a small rodlet with a 45% smaller pellet diameter while maintaining the same linear power. Therefore, the time for data collection up to high burnup can be significantly reduced while maintaining the same temperature profile, which largely determines the material response. Tests of fuel rodlets of standard and compact size will be carried out in the Idaho National Laboratory’s Advanced Test Reactor (ATR), including full size and compact rodlets with varying gap sizes. By applying physics-based mechanistic modeling and simulation in accordance with the AFQ methodology, this type of compact rodlet testing in a thermal test reactor captures the necessary phenomena to test fuel material models up to high burnup and to simulate the expected impact of fast neutron radiation on the fuel in FMR operations. Finally, this approach to testing fast reactor fuels in existing thermal test reactors, paired with advanced physics-based mechanistic modeling and simulation, is expected to be applicable to a range of advanced fuels and will decrease the overall fuel qualification timeframe from decades to years.

Advanced test reactor (ATR)↗

DOE OSTI2019

An Experimental Reversed Heat Flux Investigation of the Helium-Cooled Modular Divertor with Multiple Jets

The Georgia Institute of Technology group has performed studies to characterize the thermal hydraulics of a single “finger” module of the helium-cooled modular divertor with multiple jets (HEMJ) proposed for long-pulse magnetic fusion reactors in a helium (He) loop designed with maximum mass flow rate of 10 g/s. However, testing divertor modules at prototypical heat fluxes and temperatures remains an engineering challenge. A new larger helium loop with a maximum mass flow rate of 100 g/s, suitable for evaluating helium-cooled divertors with larger surface areas such as a nine-finger HEMJ module, is currently being constructed. This work presents an experimental validation of a numerical model exploring the applicability of the “reversed heat flux approach,” which cools (versus heats) the plasma-facing surface of the divertor module to evaluate the helium-side heat transfer coefficient (HTC). The approach is to be used for performance evaluation of single and multiple modules of HEMJ in existing and future large helium loops. A cooling facility for producing a jet of water with a maximum mass flow rate of 1.4 kg/s at a maximum pressure of 0.4 MPa and temperature of 295 K (Re = 2.2 × 10 5 ) is described. Numerical and experimental results are presented for the heat flux and average helium impingement surface temperature over a range of water flow rates (0.5 to 1.4 kg/s) for heat fluxes as high as 5 MW/m 2 . The numerical model suggests that the HTC of the water impingement surface is comparable to or greater than that of the helium impingement surface. For given helium and water temperatures, the heat flux values are generally limited by conduction across the outer shell. These initial studies provide guidance on extending this approach to estimating the thermal-hydraulic performance of larger divertor module designs while reducing the challenges associated with studying such designs in the normal heating configuration at their extremely high prototypical temperatures and incident heat fluxes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Experimental and Numerical Evaluation of the Thermal-Fluid Characteristics of the Helium-Cooled Modular Divertor with Multiple Jets Using a Reversed Heat Flux Approach

A single-finger unit of the Helium-Cooled Modular Divertor with Multiple Jets (HEMJ) with a plasma-facing surface (PFS) area of about 2 cm 2 has been studied in a helium (He) loop at He mass flow rates m˙ H ≤ 8 g/s and nearly prototypical conditions. Based on previous studies of the single finger of the HEMJ, our Georgia Institute of Technology group is planning to experimentally study larger divertors. Given that the HEMJ test section was heated with an induction heater and that it is impractical to scale this up to divertors with larger PFS areas, a reversed heat flux approach is being considered to measure heat transfer coefficients (HTCs). In this approach, the direction of the heat flux is reversed with water cooling and high-temperature He heating of the outer shell attached to the PFS. This work presents an initial experimental and numerical evaluation of this approach for a single HEMJ finger. Experiments with brass and copper-chromium-zirconium outer shells were conducted at dimensionless He mass flow rates or Reynolds numbers Re = 1 × 10 4 to 4.7 × 10 4 , an inlet pressure of 10 MPa, temperatures as great as 673 K, and maximum heat flux of 8.4 MW/m 2 . The experiments verify that the He-side HTCs are independent of the direction of the heat flux. Here, the results agree well with previous Nusselt number correlation and pressure loss coefficients for the HEMJ obtained using the normal heating approach.

42 ENGINEERING↗

DOE OSTI2023

Performance Comparison of Helium and sCO 2 as Coolants for Modular Finger-Type Divertors

Several studies at the Georgia Institute of Technology have evaluated the thermal and fluids performance of the helium-cooled modular divertor with multiple jets (HEMJ) over the past decade. This finger-type divertor was studied both experimentally at nearly prototypical conditions and numerically at fully prototypical operating conditions using experimentally validated simulations. Recently, supercritical carbon dioxide (sCO 2 ) has been studied as the primary coolant in power cycles and other applications in various systems, in part because CO 2 achieves the high densities typical of supercritical fluids at relatively low temperatures and pressures, with a critical point of (7.38 MPa, 31°C). This density makes it possible to realize very compact and efficient sCO 2 power cycles. The feasibility of sCO 2 as a coolant for plasma-facing components, specifically the divertor, was therefore evaluated as part of the Fusion Energy System Studies design study activities. This work compares the thermal-fluid performance of helium and sCO 2 in the HEMJ divertor geometry using numerical simulations at prototypical conditions: inlet temperatures T i = 600°C to 700°C, pressures p ≈ 10 MPa, and steady-state incident heat fluxes on the tile q″ < 17 MW/m 2 . The performance is quantified here as the maximum heat flux that can be accommodated by the plasma-facing tile, the pumping power fraction, defined as the ratio of the coolant pumping power to the incident thermal power, and the operating stress limits based on ASME pressure vessel criteria. As expected, helium requires lower mass flow rates and pumping power fractions within imposed maximum temperature limits for the HEMJ pressure boundary. However, it also appears that neither helium nor sCO 2 can remove 10 MW/m 2 of incident heat flux while meeting ASME pressure vessel criteria. Finally, the numerical modeling reveals that sCO 2 may remove slightly higher incident heat fluxes than helium due to the imposed stress limits due to the sCO 2 coolant resulting in smaller local temperature gradients, albeit at a considerably higher pumping power fraction.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Thermal-Fluid and Thermal-Structural Response of the T-Tube Modular Divertor to Spatiotemporally Varying Heat Loads

Tungsten (W) is the leading candidate for divertor target plates because of its high melting point (>3000°C), thermal conductivity, and ultimate tensile stress. While W and its alloys are the only solid materials that can survive the high heat fluxes incident on the divertor, W’s low-ductility high ductile-to-brittle transition temperature of ~600°C and relatively low recrystallization temperature (RT) of ~1300°C pose structural (among other) challenges. The objective of this work is to estimate the thermal-fluid and thermal-structural performance of the helium (He)-cooled T-tube divertor, which was originally developed by the Advanced Reactor Innovation and Evaluation Study (ARIES) using numerical simulations. Here, predictions of temperature distributions across the plasma-facing structural component and surface pressures from computational fluid dynamics simulations are used to determine stress distributions using commercial structural finite element modeling software over a range of fusion-relevant conditions. The maximum allowable incident heat fluxes are determined based on the temperature limits imposed by the ITER elastic Structural Design Criteria for In-vessel Components (SDC-IC) and the maximum RT over a range of He mass flow rates and presented in the form of performance design charts. Our recent work found that thermal- structural criteria accounting for the low ductility of W in a finger-type modular divertor constrain the maximum incident heat fluxes to values well below the ITER specifications, and those based on considering only the RT demonstrate that integrated thermal-fluid and elastic structural performance evaluation are required for accurate assessment of divertor performance. This novel analysis of the T-tube considers how nonuniform and transient incident heat fluxes affect its thermal-fluid and thermal-structural performance, as well as the effect of volumetric heating, which can be as great as 27% of the power incident on the divertor surface. The W tile of the T-tube, with its relatively large plasma-facing area of ~15 cm 2 , will likely experience significant spatial variations in incident heat flux. This work therefore assesses whether steady-state incident heat flux profiles with a peak of 10 MW/m 2 and maximum heat flux gradients of 200 MW/m 2 per m exceed the structural limits imposed by the ITER elastic SDC-IC and the maximum RT over a range of fusion-relevant conditions. The effect of transient heat fluxes typical of plasma detachment and reattachment from the target plate due, for example, to gas injection are also evaluated

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Toward Verification of RANS Simulations of the T-Tube Modular Divertor Using Large Eddy Simulations of Impinging Turbulent Plane Jets

Turbulent impinging jets have been proposed to cool high heat flux plasma-facing components such as the solid tungsten target plates of the divertor in long-pulse magnetic fusion energy reactors. In particular, the T-tube modular divertor, originally developed by the ARIES Team, consists of two concentric cylindrical tubes where helium flows through a slot in the inner tube, forming an approximately planar jet that impinges upon and cools the inner surface of the pressure boundary (namely, the outer tube) and the ~15-cm 2 plasma-facing W target. The objective of this work is to demonstrate that large eddy simulations (LESs) accurately simulate the thermal transport in canonical flows that comprise the cooling flow in the T-tube, as well as validate temperatures from LES with experimental measurements in a simplified T-tube geometry. Wall‑resolved LESs, validated by experimental data and verified by direct numerical simulations (DNSs), provide benchmark data for two canonical flows in the T‑tube, namely, planar impinging and wall jets, for Reynolds numbers Re B = 4 × 10 3 to 2 × 10 4 . Our LES results are within 4% to 12% root-mean-square error (RMSE) of surface Nusselt number distributions (Nu) from experiments and DNSs. The validated LES results are then used as the ground truth to evaluate four Reynolds‑averaged Navier-Stokes (RANS) turbulence closures, namely, the k‑ω SST, realizable k‑ε, GEKO, and γ‑SST models. The k‑ω SST model has the best overall performance in terms of heat transfer, giving surface Nu within 12% RMSE of the LES results for high‑ReB impinging jets and reduced overprediction in the wall‑jet region. The GEKO model with default constants has the next best performance, providing slightly better Nu predictions for low ReB impinging jets (versus k-ω SST) but worse overall performance over the full range of ReB studied here. The realizable k‑ε turbulence model significantly overestimates turbulence near the stagnation point, while the γ‑SST model suppresses near‑wall production, biasing the simulations toward simulating laminar surface heat transfer. Simulations of the simplified T‑tube show that LES and RANS simulations with the k‑ω SST model give nearly identical average heat transfer coefficients (HTCs) over the impingement surface. The realizable k‑ε model predicts significantly lower wall temperatures due to overestimation of HTC in the outlet flow.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Design and Implementation of Surface Eroding Thermocouples for Stage-One Modular Divertor Integration at the DIII-D Tokamak

The DIII-D has upgraded its upper divertor to a modular system using copper alloy pedestals to alter the divertor geometry without changing the vessel structure. Six new graphite tiles were designed for the shape and volume rise (SVR) divertor. Here, these new SVR tiles facilitated the formation of a poloidal array of 27 surface eroding thermocouples (SETCs) in the upper divertor region. At one location, a specialized recessed SETC, paired with a standard flush SETC, was installed in one of the ceiling tiles to provide comprehensive heat flux measurements, distinguishing between charged and noncharged particle contributions. Upgrades were made to the SETC system in the small-angle slot (SAS) divertor to improve overall performance. These upgrades included optimizing the feedthrough system to double the thermocouple cable capacity and reallocating cables from the SAS area to the SVR divertor. A compact isolation amplifier system with a fixed gain of 41 was employed to improve the signal level and minimize interference. Additionally, two analog-to-analog fiber systems were implemented for transmitting thermocouple signals over a single fiber, significantly reducing both noise levels and costs. The newly installed SETCs in the SVR divertor successfully completed initial commissioning testing. The SETCs captured the in-out asymmetry in the power distribution between the inner and outer strike points and demonstrated the dependency of the heat flux profile on the outer strike point location. During divertor detachment, heat flux mitigation was noted at the outer strike point location, while significant heat flux contributions from neutral particles were measured in the SVR divertor.

Divertor↗

DOE OSTI2025

Post-inflationary enhancement of adiabatic perturbations in modular cosmology

We show that multi-field inflationary models with negligible turning in field space during inflation can lead to an effective sourcing of adiabatic from entropic perturbations afterthe end of inflation. We illustrate this general phenomenon with a detailed analysis of an inflationary model whose scalar potential is determined by modular invariance. Its entropic perturbations are frozen during inflation, but instead, they are converted into adiabatic perturbations in the first post-inflationary e-folds. The curvature power spectrum, giving rise to CMB fluctuations, reaches a novel and enhanced plateau in this process; we address the implications for the inflationary observables As , n s and r.

cosmological perturbation theory↗

DOE OSTI2017

Development of a modular test system for the silicon sensor R&D of the ATLAS Upgrade

High Voltage CMOS sensors are a promising technology for tracking detectors in collider experiments. Extensive R&D studies are being carried out by the ATLAS Collaboration for a possible use of HV-CMOS in the High Luminosity LHC upgrade of the Inner Tracker detector. CaRIBOu (Control and Readout Itk BOard) is a modular test system developed to test Silicon based detectors. It currently includes five custom designed boards, a Xilinx ZC706 development board, FELIX (Front-End LInk eXchange) PCIe card and a host computer. A software program has been developed in Python to control the CaRIBOu hardware. CaRIBOu has been used in the testbeam of the HV-CMOS sensor AMS180v4 at CERN. Preliminary results have shown that the test system is very versatile. In conclusion, further development is ongoing to adapt to different sensors, and to make it available to various lab test stands.

43 PARTICLE ACCELERATORS↗

DOE OSTI2024

Development of modular expression across phylogenetically distinct diazotrophs

Diazotrophic bacteria can reduce atmospheric nitrogen into ammonia enabling bioavailability of the essential element. Many diazotrophs closely associate with plant roots increasing nitrogen availability, acting as plant growth promoters. These associations have the potential to reduce the need for costly synthetic fertilizers if they could be engineered for agricultural applications. However, despite the importance of diazotrophic bacteria, genetic tools are poorly developed in a limited number of species, in turn narrowing the crops and root microbiomes that can be targeted. Here, we report optimized protocols and plasmids to manipulate phylogenetically diverse diazotrophs with the goal of enabling synthetic biology and genetic engineering. Three broad-host-range plasmids can be used across multiple diazotrophs, with the identification of one specific plasmid (containing origin of replication RK2 and a kanamycin resistance marker) showing the highest degree of compatibility across bacteria tested. We then demonstrated modular expression by testing seven promoters and eleven ribosomal binding sites using proxy fluorescent proteins. Finally, we tested four small molecule inducible systems to report expression in three diazotrophs and demonstrated genome editing in Klebsiella michiganensis M5al.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

ClusterCAD: a computational platform for type I modular polyketide synthase design

Here, we present ClusterCAD, a web-based toolkit designed to leverage the collinear structure and deterministic logic of type I modular polyketide synthases (PKSs) for synthetic biology applications. The unique organization of these megasynthases, combined with the diversity of their catalytic domain building blocks, has fueled an interest in harnessing the biosynthetic potential of PKSs for the microbial production of both novel natural product analogs and industrially relevant small molecules. However, a limited theoretical understanding of the determinants of PKS fold and function poses a substantial barrier to the design of active variants, and identifying strategies to reliably construct functional PKS chimeras remains an active area of research. In this work, we formalize a paradigm for the design of PKS chimeras and introduce ClusterCAD as a computational platform to streamline and simplify the process of designing experiments to test strategies for engineering PKS variants. ClusterCAD provides chemical structures with stereochemistry for the intermediates generated by each PKS module, as well as sequence- and structure-based search tools that allow users to identify modules based either on amino acid sequence or on the chemical structure of the cognate polyketide intermediate. ClusterCAD can be accessed at https://clustercad.jbei.org and at http://clustercad.igb.uci.edu.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗