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DOE OSTI2020

Computational Modeling To Adapt Neutralizing Antibody

Monoclonal antibodies (mAbs) is the leading therapy for viral infections because it provides immediate protection and can be administered at higher levels than in a natural immune response. Finding mAbs that neutralize a broad spectrum of viral targets has proven difficult because many species and strains exist and blanket targeting is a slow and laborious process to experimentally screen 108 variants. A new method is needed to rapidly redesign mAbs for homologous targets. This project speeds up redesign using structure-based computational design to reduce the mAbs search space to a manageable level and screen mutants at a much higher rate than in experiments. Computation will also provide critical knowledge about the fundamental interactions. The project will adapt S230, a human antibody that neutralizes SARS-CoV, to neutralize SARS-COV-2.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2012

Computer modeling of self-assembly of the crystal structure of zeolite Na{sub 384}[Al{sub 384}Si{sub 384}O{sub 1536}] (H{sub 2}O){sub 422} (LTN, cF4080) from suprapolyhedral cluster precursors AB{sub 2} (A-K{sub 48}, B-K{sub 24})

Combinatorial and topological analyses and a simulation of the self-assembly of zeolite crystal structure Na{sub 384}Al{sub 384}Si{sub 384}O{sub 1536} {center_dot} 422H{sub 2}O (LTN, sp. gr. Fd3 bar) have been performed using computer methods (TOPOS program package). A cubic cell with the parameters a = 36.95 Angstrom-Sign and V = 50 449 Angstrom-Sign {sup 3} contains 768 framework-forming AlO{sub 4}- and SiO{sub 4} tetrahedra (T tetrahedra). The method of complete expansion of a 3D factor graph in nonintersecting cluster substructures in the tetrahedral T framework was used to reveal nanocluster precursors: A composed of 48 T tetrahedra (A-K{sub 48}) and B composed of 24 T tetrahedra (B-K{sub 24}). The nanocluster precursors A and B correspond to the polyhedral T clusters (tiles) 48T-grc and 24T-toc; they are involved in the matrix self-assembly of the crystal structure within the supracluster AB{sub 2}. The centers of clusters A and B occupy the positions of Mg and Cu atoms in the Laves net AB{sub 2} = MgCu{sub 2}; i.e., the zeolite structure is a suprapolyhedral analog of an intermetallic compound. The self-assembly code of a 3D structure from complementary bound nanocluster precursors is completely reconstuctured in the following form: supracluster {yields} primary chain {yields} microlayer {yields} microframework {yields} ...framework. The localization of the Na{sup +} template cations in the 6T- and 8T rings of nanocluster precursors A and B and Na{sup +} spacer cations in the 28T-ltn tile with the formation of tetrahedral configuration and in the center of 6-ring, which arises as a result of bonding two B nanoclusters, is established.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Computational models and experimental studies of mold filling in thin channels with yield stress fluids [Slides]

We propose developing numerical methods informed by novel experimental diagnostics that transition from solid-to-fluid, while accurately predicting the stress and deformation regardless of phase.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Computational modeling and neutron imaging to understand interface shape and solute segregation during the vertical gradient freeze growth of BaBrCl:Eu

In this work we apply continuum models to analyze phase change, heat transfer, fluid flow, solute transport, and segregation in order to understand prior neutron imaging observations of the vertical gradient freeze growth of Eu-doped BaBrCl. The models provide a rigorous framework in which to understand the mechanisms that are responsible for the complicated evolution of interface shape and dopant distribution in the growth experiment. We explain how a transition in the solid/liquid interface shape from concave to convex is driven by changes in radial heat transfer caused by furnace design. We also provide a mechanistic explanation of how dynamic growth conditions and changes of the flow structure in the melt result in complicated segregation patterns in this system. A growth pause caused by controller lock-up is shown to result in a band of solute depletion in accordance with classical theory. However, changing flow patterns during growth result in a non-monotonic axial distribution of solute that cannot be explained by simple application of classical segregation models. We assert that the approach presented here, namely the use of rigorous models in conjunction advanced diagnostics, such as neutron imaging, provides an exciting path forward for process optimization and control, accelerating the incremental advances that have, in the past, typically relied on empiricism, experience, and intuition.

36 MATERIALS SCIENCE↗

DOE OSTI2016

Computational modeling of latent-heat-storage in PCM modified interior plaster

The latent heat storage systems represent a promising way for decrease of buildings energy consumption with respect to the sustainable development principles of building industry. The presented paper is focused on the evaluation of the effect of PCM incorporation on thermal performance of cement-lime plasters. For basic characterization of the developed materials, matrix density, bulk density, and total open porosity are measured. Thermal conductivity is accessed by transient impulse method. DSC analysis is used for the identification of phase change temperature during the heating and cooling process. Using DSC data, the temperature dependent specific heat capacity is calculated. On the basis of the experiments performed, the supposed improvement of the energy efficiency of characteristic building envelope system where the designed plasters are likely to be used is evaluated by a computational analysis. Obtained experimental and computational results show a potential of PCM modified plasters for improvement of thermal stability of buildings and moderation of interior climate.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2023

FY23 Progress on Computational Modeling of the Water-Based NSTF

This report summarizes the system-level modeling effort by Argonne National Laboratory (Argonne) of the Natural convection Shutdown heat removal Test Facility (NSTF) in FY23. As a continuation of the modeling effort from FY22, this year’s work focuses on improving the RELAP5-3D model developed previously for two-phase flow simulations. The RELAP5-3D model is updated to more accurately capture the heat loss experienced by the facility. The updated model is compared against experimental data for benchmarking purposes of the RELAP5-3D input model. By correctly accounting for heat loss, the updated RELAP5-3D model can now predict the two-phase baseline case more accurately. The onset and the duration of instability are captured well by the model. Furthermore, analyses are performed to better understand the instability mechanism experienced by the flow where the expansion of the boiling boundary in the chimney is studied in details and the fundamental frequencies of the oscillations are obtained. The updated RELAP5-3D model is further compared against four fault conditions, namely the reduction of riser header inlet flow area, depletion of system inventory, blocked riser channels, and static boiling scenario. For each fault condition, minor modifications and tuning are performed to improve the predictions of the model. The purpose of the analyses is to investigate the capability of RELAP5-3D in predicting complex two-phase flows in possible accident scenarios in actual Reactor Cavity Cooling System (RCCS). Overall, the model is able to capture the behaviors and trends of these fault conditions relatively well. Some discrepancies remain between the experimental data and the predictions, many of which are likely due to the differences in the predicted and experimental vapor generation rate. Future work will focus on the continued development of the current RELAP5-3D input model of the NSTF to both improve the accuracy of the model’s predictive capability and continue supporting the experimental program needs. The mutually beneficial relationship between analysis and experimental efforts has become integral to the parent NSTF program, and the greater objective to fully understand and accurately predict the heat removal performance of a full scale RCCS concept.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2024

Computational Modeling of CO2 Capture By Novel PIM-RU in a Fluidized Bed Riser

The interest in carbon capture, storage, and utilization (CCUS) has increased significantly in the past few decades as it can help mitigate the threat of global warming caused by substantial increase in CO2 emissions due to anthropogenic activities. Although several CO2 capture technologies have been developed, porous solid sorbents, which adsorb CO2 by physisorption, are considered promising candidates for post-combustion CO2 capture because of the easier recovery of adsorbed CO2 and high material stability. Some prominent types of porous solid sorbents are metal-organic frameworks (MOFs), Zeolite, mesoporous silica, and polymer-based sorbents (e.g., polymers with intrinsic microporosity or PIM). Oak Ridge National Laboratory (ORNL) recently developed a novel PIM-based sorbent, referred to here as PIM-RU. The main objective of this work is to investigate the CO2 capture performance of this sorbent using computational fluid dynamics (CFD). While process configuration and reactor design are open questions, a fluidized bed riser was selected as the contactor type for this study.

Aziz, Hossain↗

DOE OSTI2015

Hydrogen-Bonding Network and OH Stretch Vibration of Cellulose: Comparison of Computational Modeling with Polarized IR and SFG Spectra

Hydrogen bonds play critical roles in noncovalent directional interactions determining the crystal structure of cellulose. Although diffraction studies accurately determined the coordinates of carbon and oxygen atoms in crystalline cellulose, the structural information on hydrogen atoms involved in hydrogen-bonding is still elusive. This could be complemented by vibrational spectroscopy; but the assignment of the OH stretch peaks has been controversial. In this study, we performed calculations using density functional theory with dispersion corrections (DFT-D2) for the cellulose Iβ crystal lattices with the experimentally determined carbon and oxygen coordinates. DFT-D2 calculations revealed that the OH stretch vibrations of cellulose are highly coupled and delocalized through intra- and interchain hydrogen bonds involving all OH groups in the crystal. Additionally, molecular dynamics (MD) simulations of a single cellulose microfibril showed that the conformations of OH groups exposed at the microfibril surface are not well-defined. Finally, comparison of the computation results with the experimentally determined IR dichroism of uniaxially aligned cellulose microfibrils and the peak positions of various cellulose crystals allowed unambiguous identification of OH stretch modes observed in the vibrational spectra of cellulose.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Procedure for the Computational Models created for the DOE/NRC Collaboration for Criticality Safety Support for Commercial-Scale HALEU Fuel Cycles Project (DNCSH)

This procedure outlines the application models developed as part of the US Department of Energy (DOE) and Nuclear Regulatory Commission (NRC) collaboration for criticality safety support for commercial scale HALEU fuel cycle and transportation (DNCSH) project, an effort authorized by the US Congress. The project is a joint effort among the DOE, NRC, numerous national laboratories, and private enterprises with project management from Oak Ridge National Laboratory.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2017

CHROTRAN: a mathematical and computational model for in situ heavy metal remediation in heterogeneous aquifers

Groundwater contamination by heavy metals is a critical environmental problem for which in situ remediation is frequently the only viable treatment option. For such interventions, a three-dimensional reactive transport model of relevant biogeochemical processes is invaluable. To this end, we developed a model, CHROTRAN, for in situ treatment, which includes full dynamics for five species: a heavy metal to be remediated, an electron donor, biomass, a nontoxic conservative bio-inhibitor, and a biocide. Direct abiotic reduction by donor-metal interaction as well as donor-driven biomass growth and bio-reduction are modeled, along with crucial processes such as donor sorption, bio-fouling and biomass death. Our software implementation handles heterogeneous flow fields, arbitrarily many chemical species and amendment injection points, and features full coupling between flow and reactive transport. We describe installation and usage and present two example simulations demonstrating its unique capabilities. One simulation suggests an unorthodox approach to remediation of Cr(VI) contamination.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

High Fidelity Computational Model for Fluidized Bed Experiments (Final Report)

MFiX was integrated with preconditioners and linear solver packages in Trilinos via MFIX, Fortran, C, and C++ wrappers. The MFIX wrapper interpreted the structure of the matrix and vector from MFiX while the Fortran wrapper transfers this information to a low-level language, C. C-wrapper transforms the memory semantic between Fortran and C++ language. C++ wrapper passes the matrix and vector to a Trilinos package and gets the solution. This solution was transferred to MFiX via C++, C, Fortran, MFIX wrapper. The framework is used to integrate first, second and third generation linear solvers in Trilinos with MFiX.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Nanoindentation Stress–Strain for Fracture Analysis and Computational Modeling for Hardness and Modulus

Stress–Strain plots based on nanoindentation load–depth curves were obtained to study phenomena like internal fracture and ductile to brittle transitions. Fracture phenomena during the indentation process were analyzed based on the stress–strain plots. A transition from ductile to brittle fracture was observed on increasing the depth or load of indenter penetration. A new approach with shape factors in the fracture studies based on radial crack branching and micro-cracking was done. Hardness and modulus plots were fitted with polynomials. The fitting parameters were varied to obtain different hardness and modulus responses.

36 MATERIALS SCIENCE↗

DOE OSTI2023

High Fidelity Computational Model for Fluidized Bed Experiments (Final Report)

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2022

Computational Modeling and Simulation for Nonproliferation: The History (and Present) of Monte Carlo and the MCNP(R) Code at Los Alamos [Slides]

The emergence of the Monte Carlo method as a research tool springs from work done at Los Alamos in the 1940s.Monte Carlo and the MCNP Code have been and continue to be developed at Los Alamos for many decades. From basic science in support of understanding nuclear interaction physics to global security applications, application uses of the code are extensive. Recent R&D projects and code modernization efforts make the MCNP code a great tool for nuclear nonproliferation applications. In collaboration with nuclear safeguards experts, new training has just recently been developed to help new practitioners learn how to use the code for nuclear safeguards applications.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

Computational Modeling of Degradation of Substituted Benzyltrimethyl Ammonium: Preprint

The degradation of cations on the alkaline exchange membranes is the major challenge for alkaline membrane fuel cells. In this paper, we investigated the degradation barriers by density functional theory for substituted benzyltrimethyl ammonium (BTMA+) cations, which is one of the most commonly used cations for alkaline exchange membranes. We found that substituted cations with electron-releasing substituent groups at meta-position of the benzyl ring could result in improved degradation barriers. However, after investigating more than thirty substituted BTMA+ cations with ten different substituent groups, the largest improvement of degradation barriers is only 1.6 kcal/mol. This implies that the lifetime of alkaline membrane fuel cells could increase from a few months to a few years by using substituted BTMA+ cations, an encouraging but still limited improvement for real-world applications.

30 DIRECT ENERGY CONVERSION↗

DOE OSTI2024

Augmenting a Simulation Campaign for Hybrid Computer Model and Field Data Experiments

The Kennedy and O’Hagan (KOH) calibration framework uses coupled Gaussian processes (GPs) to meta-model an expensive simulator (first GP), tune its “knobs” (calibration inputs) to best match observations from a real physical/field experiment and correct for any modeling bias (second GP) when predicting under new field conditions (design inputs). There are well-established methods for placement of design inputs for data-efficient planning of a simulation campaign in isolation, that is, without field data: space-filling, or via criterion like minimum integrated mean-squared prediction error (IMSPE). Analogues within the coupled GP KOH framework are mostly absent from the literature. Here, in this study, we derive a closed form IMSPE criterion for sequentially acquiring new simulator data for KOH. We illustrate how acquisitions space-fill in design space, but concentrate in calibration space. Closed form IMSPE precipitates a closed-form gradient for efficient numerical optimization. We demonstrate that our KOH-IMSPE strategy leads to a more efficient simulation campaign on benchmark problems, and conclude with a showcase on an application to equilibrium concentrations of rare earth elements for a liquid–liquid extraction reaction.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Computational Modeling of Water Infiltration From Ditches Into Roadway Embankments

Ditches are built along roadways to convey the stormwater runoff. They collect the runoff from the pavement and adjacent drainage areas. Water can move freely in a ditch away from the road surface, thus making it safer for the vehicular traffic. South Carolina DOT expressed interest in studying infiltration of water from ditches into roadway embankments. As part of the current design criteria, it is recommended that the road subgrades be 1.0 foot above the design event water surface elevation in the ditch. The distance between the water surface and bottom of the subbase is referred to as “freeboard”. The purpose of this requirement is to lower the risk of pavement damage by moving the flow away from the pavement, containing the captured flow, and conveying flow received from adjacent properties to outfalls. With changes in roadway design standards, larger shoulders and flatter cross-slopes have moved ditches further away from the pavement and the subbase. These changes could allow for a lower freeboard standard without reducing safety margins due to the increased lateral distance from the subbase to the ditch. The objective of this study is to evaluate whether the current SCDOT criterion requiring the roadway subgrade to be 1 ft above the design-event ditch water surface can be relaxed under selected geometric and soil conditions, particularly where larger shoulder widths and flatter side slopes increase horizontal separation between ditch water and pavement structure.

42 ENGINEERING↗

DOE OSTI2015

Computational Modeling of Mixed Solids for CO2 CaptureSorbents

Since current technologies for capturing CO2 to fight global climate change are still too energy intensive, there is a critical need for development of new materials that can capture CO2 reversibly with acceptable energy costs. Accordingly, solid sorbents have been proposed to be used for CO2 capture applications through a reversible chemical transformation. By combining thermodynamic database mining with first principles density functional theory and phonon lattice dynamics calculations, a theoretical screening methodology to identify the most promising CO2 sorbent candidates from the vast array of possible solid materials has been proposed and validated. The calculated thermodynamic properties of different classes of solid materials versus temperature and pressure changes were further used to evaluate the equilibrium properties for the CO2 adsorption/desorption cycles. According to the requirements imposed by the pre- and post- combustion technologies and based on our calculated thermodynamic properties for the CO2 capture reactions by the solids of interest, we were able to screen only those solid materials for which lower capture energy costs are expected at the desired pressure and temperature conditions. Only those selected CO2 sorbent candidates were further considered for experimental validations. The ab initio thermodynamic technique has the advantage of identifying thermodynamic properties of CO2 capture reactions without any experimental input beyond crystallographic structural information of the solid phases involved. Such methodology not only can be used to search for good candidates from existing database of solid materials, but also can provide some guidelines for synthesis new materials. In this presentation, we apply our screening methodology to mixing solid systems to adjust the turnover temperature to help on developing CO2 capture Technologies.

CO2 solid sorbents, ab initio thermodynamics, firs↗