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At least 379 records · Page 21

Design, scaling and cost evaluations of circulating fluidized-bed systems for biomass pyrolysis

To generate updated and transparent capital cost estimates for biomass fast pyrolysis equipment, refinery fluidized catalytic cracking design and sizing principles are examined and extended to pyrolysis of woody biomass. Capital costs for the sized equipment are estimated with process-industry software. A one-dimensional flow simulation with pyrolysis kinetics is leveraged to validate the fluidization conditions and thermal energy balance. After successful sizing and a system cost estimate of $\$$2.8 M (in 2016 US$\$$) at the biorefinery scale of 1000 metric tons per day (MTD), these methods were exercised for even smaller equipment at the distributed pyrolysis scale with modifications to the process design constraints, and not directly comparable with the 1000 MTD case, arriving at capital cost estimates of $\$$1.2 M for a 500 ton/day system and $\$$0.9 M for a 200 ton/day system. Here in this work, It is noted that this work only estimates purchased equipment costs at the ±50% accuracy level; there are significant other custom factors applicable to each installation based on location, maturity, scale, complexities during installation, engineering and licensing costs, etc. that need to be added on to these estimates to derive investment costs.

09 BIOMASS FUELS↗

SEC ‐ SAXS / MC Ensemble Structural Studies of the Microtubule Binding Protein Cdt1 Show Monomeric, Folded‐Over Conformations

ABSTRACT Cdt1 is a mixed folded protein critical for DNA replication licensing and it also has a “moonlighting” role at the kinetochore via direct binding to microtubules and the Ndc80 complex. However, it is unknown how the structure and conformations of Cdt1 could allow it to participate in these multiple, unique sets of protein complexes. While robust methods exist to study entirely folded or unfolded proteins, structure–function studies of combined, mixed folded/disordered proteins remain challenging. In this work, we employ orthogonal biophysical and computational techniques to provide structural characterization of mitosis‐competent human Cdt1. Thermal stability analyses shows that both folded winged helix domains1 are unstable. CD and NMR show that the N‐terminal and linker regions are intrinsically disordered. DLS shows that Cdt1 is monomeric and polydisperse, while SEC‐MALS confirms that it is monomeric at high concentrations, but without any apparent inter‐molecular self‐association. SEC‐SAXS enabled computational modeling of the protein structures. Using the program SASSIE, we performed rigid body Monte Carlo simulations to generate a conformational ensemble of structures. We observe that neither fully extended nor extremely compact Cdt1 conformations are consistent with SAXS. The best‐fit models have the N‐terminal and linker disordered regions extended into the solution and the two folded domains close to each other in apparent “folded over” conformations. We hypothesize the best‐fit Cdt1 conformations could be consistent with a function as a scaffold protein that may be sterically blocked without binding partners. Our study also provides a template for combining experimental and computational techniques to study mixed‐folded proteins.

Cell Biology↗

iSPECTRON: a simulation interface for linear and nonlinear spectra with ab-initio quantum chemistry software

We introduce iSPECTRON, an open source (under the Educational Community License version 2.0) program that parses data from common quantum chemistry software (NWChem, OpenMolcas, Gaussian, Cobramm, etc.), produces the input files for the simulation of linear and nonlinear spectroscopy of molecules with the Spectron code, and analyzes the spectra with a broad range of tools. Vibronic spectra are expressed in term of the electronic eigenstates, obtained through quantum chemistry computations, and vibrational/bath effects are incorporated in the framework of the displaced harmonic oscillator model, where all required quantities are computed at the Franck-Condon point. The code capabilities are illustrated by simulating linear absorption, transient absorption and two dimensional electronic spectra of the pyrene molecule. Two levels of electronic structure theory, TDDFT (with NWChem) and RASSCF/RASPT2 (with OpenMolcas), are compared where possible. Acknowledgements: F.S., A.N., D.R.N., N.G., S.M, M.G. acknowledge support from the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division under Award Nos. DE-SC0019484, KC-030103172684. The Spectron code was developed with support from the National Science Foundation (Grant CHE- 1953045). This research benefited from computational resources provided by EMSL, a DOE Office of Science User Facility sponsored by the Office of Biological and Environmental Research and located at PNNL. PNNL is operated by Battelle Memorial Institute for the United States Department of Energy under DOE Contract No. DE-AC05-76RL1830.

Segatta, Francesco↗

X‐ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double‐strand break repair impacting cell and cancer biology

Abstract Evolutionary selection ensures specificity and efficiency in dynamic metastable macromolecular machines that repair DNA damage without releasing toxic and mutagenic intermediates. Here we examine non‐homologous end joining (NHEJ) as the primary conserved DNA double‐strand break (DSB) repair process in human cells. NHEJ has exemplary key roles in networks determining the development, outcome of cancer treatments by DSB‐inducing agents, generation of antibody and T‐cell receptor diversity, and innate immune response for RNA viruses. We determine mechanistic insights into NHEJ structural biochemistry focusing upon advanced small angle X‐ray scattering (SAXS) results combined with X‐ray crystallography (MX) and cryo‐electron microscopy (cryo‐EM). SAXS coupled to atomic structures enables integrated structural biology for objective quantitative assessment of conformational ensembles and assemblies in solution, intra‐molecular distances, structural similarity, functional disorder, conformational switching, and flexibility. Importantly, NHEJ complexes in solution undergo larger allosteric transitions than seen in their cryo‐EM or MX structures. In the long‐range synaptic complex, X‐ray repair cross‐complementing 4 (XRCC4) plus XRCC4‐like‐factor (XLF) form a flexible bridge and linchpin for DNA ends bound to KU heterodimer (Ku70/80) and DNA‐PKcs (DNA‐dependent protein kinase catalytic subunit). Upon binding two DNA ends, auto‐phosphorylation opens DNA‐PKcs dimer licensing NHEJ via concerted conformational transformations of XLF‐XRCC4, XLF–Ku80, and LigIV BRCT –Ku70 interfaces. Integrated structures reveal multifunctional roles for disordered linkers and modular dynamic interfaces promoting DSB end processing and alignment into the short‐range complex for ligation by LigIV. Integrated findings define dynamic assemblies fundamental to designing separation‐of‐function mutants and allosteric inhibitors targeting conformational transitions in multifunctional complexes.

59 BASIC BIOLOGICAL SCIENCES↗

Fragme∩t: An Open‐Source Framework for Multiscale Quantum Chemistry Based on Fragmentation

Fragment-based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations, by partitioning a large calculation into smaller subsystems then considering the many-body interactions between them. Variants of this approach have been used to parameterize classical force fields and machine learning potentials, applications that benefit from interoperability between quantum chemistry codes. However, there is a dearth of software that provides interoperability yet is purpose-built to handle the combinatorial complexity of fragment-based calculations. To fill this void we introduce “Fragme∩t”, an open-source software application that provides a tool for community validation of fragment-based methods, a platform for developing new approximations, and a framework for analyzing many-body interactions. Fragme∩t includes algorithms for automatic fragment generation and structure modification, and for distance- and energy-based screening of the requisite subsystems. Checkpointing, database management, and parallelization are handled internally and results are archived in a portable database. Interfaces to various quantum chemistry engines are easy to write and exist already for Q-Chem, PySCF, xTB, Orca, CP2K, MRCC, Psi4, NWChem, GAMESS, and MOPAC. Applications reported here demonstrate parallel efficiencies around 96% on more than 1000 processors but also showcase that the code can handle large-scale protein fragmentation using only workstation hardware, all with a codebase that is designed to be usable by non-experts. Fragme∩t conforms to modern software engineering best practices and is built upon well established technologies including Python, SQLite, and Ray. The source code is available under the Apache 2.0 license.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Digital Twins for Nuclear Power Plants and Facilities

The nuclear digital twin (DT) is the virtual representation of a nuclear energy system across its lifecycle. The nuclear DT uses real-time information and other data sources to improve the process of design, licensing, construction, security, O&M, decommissioning, and waste disposal. By leveraging the knowledge base and experience from the past 40 years of LWR operation, the nuclear DT is helping to accelerate the development and deployment of advanced nuclear technology in areas of passive safety, new fuel forms, instrumentation, and reactor control. For the currently operating nuclear fleet, DTs are reducing the operational risks, increasing plant availability, increasing energy capability, and reducing electricity production costs. For advanced fission and fusion reactors, DTs are being used to design for passive safety and built-in security-by-design. Rapidly deployable small modular reactor (SMR) and microreactor designs compatible with modular construction techniques and advanced manufacturing will be the new normal, reducing the need for large capital expenditures and compressing construction schedules. In addition, lower operational and maintenance costs will be realized by reducing the complexity of operations, staffing needs, and maintenance-related activities.

Kropaczek, Dave↗

A Comprehensive Scientific Survey of Excipients Used in Currently Marketed, Therapeutic Biological Drug Products

The steady development of biotechnology-derived therapeutic biologics over the last few decades has generated drugs that are now standard medical treatments for a range of indications. While the development of protein products has surged in recent years, the formulation and delivery of these complex molecules have relied on drug-specific studies and, in some instances, data from non-proteinaceous drug products. The commonalities, trends, and gaps in excipient technologies used to support the development of therapeutic proteins largely remain unexplored due to the drug-specific nature of many formulations. Using a comprehensive and relational database approach, we aimed to provide a scientific survey of all approved or licensed biotechnology-derived drug products with the goal of providing evidence-based information on common attributes and trending features in protein product excipients. We examined 665 formulations, and 395 unique formulations based on having unique excipients within them, that supported 211 therapeutic proteins as of June 2020. We report the prevalence of each excipient class and excipient chemical used in eight different drug types including monoclonal antibodies, antibody conjugates, cytokines and growth factors, enzymes, polypeptide hormones, pulmonary surfactants, recombinant fusion proteins, and toxins. We also report the prevalence by excipient type among all therapeutic proteins, in the context of each drug’s recommended pH range, concentration ranges for excipients, and route of administration. The results of our analyses indicate certain excipients common to monoclonal antibodies, cytokines, and polypeptide hormones. We also report on excipients unique to protein drug products, such as amino acids, solubilizers, and lyoprotectants. Overall, our report summarizes the current landscape of excipients used in marketed biotechnology-derived therapeutic biologic products.

60 APPLIED LIFE SCIENCES↗

Implementing a unified solver for nonlinearly constrained optimization

SQP and interior-point methods (also referred to as Lagrange-Newton methods) typically share key algorithmic components, such as strategies for computing descent directions and mechanisms that promote global convergence. Building on this insight, we introduce a unifying framework with eight building blocks that abstracts the workflows of Lagrange-Newton methods. We then present Uno, a modular C++ solver that implements our unifying framework and allows the automatic combination of a wide range of strategies with no programming effort from the user. Uno is meant to (1) organize mathematical optimization strategies into a coherent hierarchy; (2) offer a wide range of efficient and robust methods that can be compared for a given instance; (3) enable researchers to experiment with novel optimization strategies; and (4) reduce the cost of development and maintenance of multiple optimization solvers. Uno’s software design allows user to compose new customized solvers for emerging optimization areas such as robust optimization or optimization problems with complementarity constraints, while building on reliable nonlinear optimization techniques. We demonstrate that Uno is highly competitive against state-of-the-art solvers filterSQP, IPOPT, SNOPT, MINOS, LANCELOT, LOQO, and CONOPT on a subset of 429 small problems from the CUTE collection. Uno is available as open-source software under the MIT license at https://github.com/cvanaret/Uno and via its C, Julia, Python, Fortran, and AMPL interfaces.

97 MATHEMATICS AND COMPUTING↗

Multicomponent gas mixture parametric CFD study of condensation heat transfer in small modular reactor system safety

Safety is always the primary concern for designing and analyzing nuclear reactor systems. The requirements for the safety margin for advanced small modular reactor (SMR) systems are targeted even higher than the conventional commercial large-scale nuclear reactors incorporating the passive and inherent safety systems. The SMR systems are designed with the condensation passive containment cooling system (PCCS), which plays a critical role in removing reactor heat during a steam release accident case. However, the presence of non-condensable gas (NCG), like air, reduces the heat transfer performance. This physics phenomenon becomes multifactorial for nuclear reactor containment during a fuel failure accident case that releases hydrogen gas. Besides, the mixture component of steam-air-hydrogen varies in reactor accident cases, which need simulation and validation keeping parameters of importance. Reviews showed that previous studies for SMR’s PCCCS did not cover the condensation heat transfer (CHT) in the presence of multicomponent NCG mixture parametric computational fluid dynamics (CFD) simulation and validation, making a research gap in the SMR design safety. A comprehensive CHT parametric CFD study was performed for SMR PCCS to fill this research gap. This study used experimental data as simulation 3D physics domain inlet and outlet boundary conditions. However, the wall boundary conditions were constant temperature, curve-fit, and annular coolant for verifying the turbulence models. Parametric simulations were performed, verified, and optimized for steam-NCGs mixtures. The multicomponent gases, multiphase mixtures, and fluid film condensation models were applied with associated turbulence models. The results of the parametric study were evaluated for realistic reactor conditions. Results showed that parametric study provided critical insight about the dependency of multicomponent gas mixture parameters that supports reactor safety design, analysis, and licensing.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Hazard analysis for identifying common cause failures of digital safety systems using a redundancy-guided systems-theoretic approach

Replacing the existing aging analog instrumentation and control (I&C) systems with modern safety control and protection, digital technology offers one of the foremost means of performance improvements and cost reductions for the existing nuclear power plants (NPPs). However, the qualification of digital I&C systems remains a challenge, especially considering the issue of software common-cause failures (CCFs), which are difficult to address. With the application and upgrades of advanced digital I&C systems, software CCFs have become a potential threat to plant safety because most redundant designs use similar digital platforms or software in the operating and application systems. With complex designs of multilayer redundancy to meet the single-failure criterion, digital I&C safety systems (e.g., engineered safety-features actuation system [ESFAS]) are of a particular concern in the U.S. Nuclear Regulatory Commission (NRC) licensing procedures. Here, this paper applies a modularized approach to conduct redundancy-guided systems-theoretic hazard analysis for an advanced digital ESFAS with multilevel redundancy designs. Systematic methods and risk-informed tools are incorporated to address both hardware and software CCFs, which provide guidance to eliminate the causal factors of potential single points of failure in the design of digital safety systems in advanced plant designs.

42 ENGINEERING↗

Multiphysics modeling of a critical dual-purpose canister in a saturated geological repository

Dual purpose dry cask storage canisters for spent nuclear fuel are designed for storage and transportation, but are not licensed for permanent disposal in a geological repository. If dual purpose canisters were to be used to dispose of spent nuclear fuel in a geological repository, they would be expected to eventually breach and be flooded with groundwater, and it is shown that some fraction of these canisters will achieve criticality. In order to evaluate the consequences of canisters going critical in a repository, an initial capability has been developed for estimating the quasi-static power level of a critical canister using loosely coupled multiphysics simulations. The low power level in a critical canister enables coupling through precomputed physics proxies. This calculated power level is then used to compute the change in the critical canister’s isotopic inventory as a function of time. Three as-loaded canisters are evaluated and two were found to have power levels below 4 kW, with a modest effect on the radiological inventory over time. This effort also shows that although some DPCs will have extremely peaked power shapes, the relatively low power and long-time scales result in relatively homogenized thermohydraulic properties in the water within the DPC.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Fast neutron irradiation capability in existing thermal test reactors

In today’s nuclear industry, momentum towards the design, licensing, and construction of advanced nuclear demonstration plants, including fast reactors, is at a remarkably high level. However, there are currently no dedicated fast spectrum irradiation test facilities in the United States to support the development of fast spectrum technologies. As a result, a unique situation is developing where most of these plants will likely be designed by leveraging historic nuclear material technologies, but where the further optimization and advancement is impeded by the lack of fast neutron irradiation test facilities. While these circumstances present a challenge, there are some near-term opportunities that, if seized, can still help develop advanced fast reactor materials to a meaningful level of readiness to support future commercial fast reactors. Here, in this paper, we assess the feasibility of using thermal neutron filtering materials in existing experiment positions in the Advanced Test Reactor (ATR) at Idaho National Laboratory and the High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory to simulate fast reactor test environments for nonfuel test specimens. Items investigated include the incident neutron flux (both fast and thermal), the total neutron fluence and cumulative atom displacements, helium production rate due to thermal neutron capture in nickel, and the potential impact that the thermal neutron filter material has on the cycle length of a given reactor. It is concluded that while HFIR provides the highest fast flux of all the options investigated, it is limited in the amount of thermal neutron filtering material that can be introduced into an experiment position without significantly affecting the operation of the reactor. Irradiation in Outboard-A positions in the ATR was found to be the most realistic near-term experiment avenue due to having ample space for several capsules in a moderately fast flux.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Genetic algorithm optimization of nuclear criticality experiment for reduction of intermediate-energy 239 Pu nuclear data uncertainties

Nuclear criticality experiments are conducted to investigate specific nuclear data important for safe handling and storage of fissile materials, reactor design and operation, and the validation of radiation transport codes. Incorrect or uncertain nuclear data can prohibitively impact operational safety limits, reactor licensing, and predictive simulation capability; therefore, integral measurements from criticality experiments are necessary and should be performed frequently. To maximize the impact of the integral measurements, it is important to consider experiment geometry, material selection, and component dimensions. When taking these considerations into account, the experiment design process becomes iterative and very time intensive. This work utilizes a genetic algorithm to efficiently explore potential nuclear criticality experiment designs for the Laboratory Directed Research & Development project PARADIGM (PARallel Approach of Differential and InteGral Measurements) at Los Alamos National Laboratory. In this paper, the building blocks of the genetic algorithm are discussed in detail, the genetic algorithm methodology is verified, and the genetic algorithm is used to produce three candidate experiment models for the final PARADIGM design. The three candidate models produced by the genetic algorithm consist of copper-reflected assemblies containing 14 repeating units of alumina, graphite, boron, and plutonium plates. Furthermore, in addition to the optimization results, final design considerations are also discussed for designs with a height and/or weight very close to or slightly above assembly machine operational limits.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

MADLens, a python package for fast and differentiable non-Gaussian lensing simulations

Here, we present MADLens a python package for producing non-Gaussian lensing convergence maps at arbitrary source redshifts with unprecedented precision. MADLens is designed to achieve high accuracy while keeping computational costs as low as possible. A MADLens simulation with only particles produces convergence maps whose power agrees with theoretical lensing power spectra up to within the accuracy limits of HaloFit. This is made possible by a combination of a highly parallelizable particle-mesh algorithm, a sub-evolution scheme in the lensing projection, and a machine-learning inspired sharpening step. Further, MADLens is fully differentiable with respect to the initial conditions of the underlying particle-mesh simulations and a number of cosmological parameters. These properties allow MADLens to be used as a forward model in Bayesian inference algorithms that require optimization or derivative-aided sampling. Another use case for MADLens is the production of large, high resolution simulation sets as they are required for training novel deep-learning-based lensing analysis tools. We make the MADLens package publicly available under a Creative Commons License

79 ASTRONOMY AND ASTROPHYSICS↗

Symbolic construction of the chemical Jacobian of quasi-steady state (QSS) chemistries for Exascale computing platforms

The Quasi-Steady State Approximation (QSSA) can be an effective tool for reducing the size and stiffness of chemical mechanisms for implementation in computational reacting flow solvers. However, for many applications, the resulting model still requires implicit methods for efficient time integration. Here, in this paper, we outline an approach to formulating the QSSA reduction that is coupled with a strategy to generate C++ source code to evaluate the net species production rates, and the chemical Jacobian. The code-generation component employs a symbolic approach enabling a simple and effective strategy to analytically compute the chemical Jacobian. For computational tractability, the symbolic approach needs to be paired with common subexpression elimination which can negatively affect memory usage. Several solutions are outlined and successfully tested on a 3D multipulse ignition problem, thus allowing portable application across chemical model sizes and GPU capabilities. The implementation of the proposed method is available at https://github.com/AMReX-Combustion/PelePhysics under an open-source license.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computational synthesis of 2D materials: A high-throughput approach to materials design

2D materials find promising applications in next-generation devices, however, large-scale, low-defect, and reproducible synthesis of 2D materials remains a challenging task. Here, to assist in the selection of suitable substrates for the synthesis of as-yet hypothetical 2D materials, we have developed an open-source high-throughput workflow package, Hetero2d, that searches for low-lattice mismatched substrate surfaces for any 2D material and determines the stability of these 2D-substrate heterostructures using density functional theory (DFT) simulations. Hetero2d automates the generation of 2D-substrate heterostructures, the creation of DFT input files, the submission and monitoring of computational jobs on supercomputing facilities, and the storage of relevant parameters alongside the post-processed results in a MongoDB database. We demonstrate the capability of Hetero2d in identifying stable 2D-substrate heterostructures for four 2D materials, namely 2H-MoS 2 , 1T- and 2H-NbO 2 , and hexagonal-ZnTe, considering 50 cubic elemental substrates. We find Cu, Hf, Mn, Nd, Ni, Pd, Re, Rh, Sc, Ta, Ti, V, W, Y, and Zr substrates sufficiently stabilize the formation energies of these 2D materials, with binding energies in the range of ~0.1–0.6 eV/atom. Upon examining the z-separation, the charge transfer, and the electronic density of states at the 2D-substrate interface, we find a covalent type bonding at the interface which suggests that these substrates can be used as contact materials for the 2D materials. Hetero2d is available on GitHub as an open-source package under the GNU license.

36 MATERIALS SCIENCE↗

Genarris 2.0: A Random Structure Generator for Molecular Crystals

Genarris is an open source Python package for generating random molecular crystal structures with physical constraints for seeding crystal structure prediction algorithms and training machine learning models. Here we present a new version of the code, containing several major improvements. A MPI-based parallelization scheme has been implemented, which facilitates the seamless sequential execution of user-defined workflows. A new method for estimating the unit cell volume based on the single molecule structure has been developed using a machine-learned model trained on experimental structures. A new algorithm has been implemented for generating crystal structures with molecules occupying special Wyckoff positions. A new hierarchical structure check procedure has been developed to detect unphysical close contacts efficiently and accurately. New intermolecular distance settings have been implemented for strong hydrogen bonds. To demonstrate these new features, we study two specific cases: benzene and glycine. Genarris finds the experimental structures of the two polymorphs of benzene and the three polymorphs of glycine. Program summary Program Title: Genarris 2.0 Program Files doi: http://dx.doi.org/10.17632/grx6mz4pjn.1 Licensing provisions: BSD-3 Clause Programming language: Python, C External routines/libraries: Spglib, ASE, pymatgen, SciPy, mpi4py, scikit-learn, PyTorch, FHI-aims. Nature of problem: Molecular crystal structure prediction. Solution method: Genarris 2.0 generates molecular crystal structures over the 230 space groups, on general and special Wyckoff positions, using physical constraints. Down-sampling of the generated structures may be performed subsequently, based on molecular crystal packing descriptors and an unsupervised machine learning algorithm. Lastly, ab initio structure relaxation may be performed for the final pool. Depending on the user-defined workflow implemented, Genarris may be used to generate diverse molecular crystal datasets to seed evolutionary algorithms or to train machine learning algorithms or as a standalone crystal structure prediction method. Restrictions: For crystal structure generation, the molecule of interest must be semi-rigid with no bond rotational degrees of freedom. Unusual features: Genarris 2.0 is a highly distributed program, making use of MPI for Python parallelization. The user has the ability to design and implement workflows by executing a user-defined list of procedures. Genarris 2.0 offers new features including a machine learning model for estimating the molecular volume in the solid state from the single molecule structure, structure generation in special Wyckoff positions of space groups, hierarchical structure checks including rigorous treatment of non-orthogonal structures, and clustering and down-selection workflows combining first principles simulations with machine learning. (C) 2020 Elsevier B.V. All rights reserved.

Crystal structure prediction↗