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DOE OSTI2018

High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow

BackgroundCancer is a complex, multiscale dynamical system, with interactions between tumor cells and non-cancerous host systems. Therapies act on this combined cancer-host system, sometimes with unexpected results. Systematic investigation of mechanistic computational models can augment traditional laboratory and clinical studies, helping identify the factors driving a treatment's success or failure. However, given the uncertainties regarding the underlying biology, these multiscale computational models can take many potential forms, in addition to encompassing high-dimensional parameter spaces. Therefore, the exploration of these models is computationally challenging. We propose that integrating two existing technologiesone to aid the construction of multiscale agent-based models, the other developed to enhance model exploration and optimizationcan provide a computational means for high-throughput hypothesis testing, and eventually, optimization.ResultsIn this paper, we introduce a high throughput computing (HTC) framework that integrates a mechanistic 3-D multicellular simulator (PhysiCell) with an extreme-scale model exploration platform (EMEWS) to investigate high-dimensional parameter spaces. We show early results in applying PhysiCell-EMEWS to 3-D cancer immunotherapy and show insights on therapeutic failure. We describe a generalized PhysiCell-EMEWS workflow for high-throughput cancer hypothesis testing, where hundreds or thousands of mechanistic simulations are compared against data-driven error metrics to perform hypothesis optimization.ConclusionsWhile key notational and computational challenges remain, mechanistic agent-based models and high-throughput model exploration environments can be combined to systematically and rapidly explore key problems in cancer. These high-throughput computational experiments can improve our understanding of the underlying biology, drive future experiments, and ultimately inform clinical practice.

Agent-based model↗

DOE OSTI2024

Sequential formulation of all‐way coupled finite strain thermoporomechanics for largely deformable gas hydrate deposits

We develop a numerically stable sequential formulation of thermoporomechanics for largely deformable gas hydrate deposits, extended from the fixed stress split of infinitesimal transformation. Constitutive equations are based on the total Lagrangian approach for both flow and geomechanics, including dynamic full tensor permeability and thermal conductivity updated from the deformation gradient. For space discretization, we take the cell-centered finite volume and node-based finite element method for flow and geomechanics, respectively. Then, we propose a sequential implicit method for all-way coupled thermoporomechanics, where the nonisothermal multiphase flow problem of gas hydrates is solved implicitly first and then the geomechanics problem is solved implicitly at the next step. During solution of the flow problem, we fix the rate of first Pioal total stress for numerical stability as well as apply porosity correction and entropy correction to account for geomechanical effects. We test numerical examples where flow and geomechanics parameters are based on deep oceanic gas hydrate deposits. When applying depressurization, even though the results between the infinitesimal transformation and finite strain geomechanics are similar in the early stages due to small deformation, we find differences between them in the late times as deformation becomes large. Accordingly, permeability and thermal conductivity tensors become nonisotropic full tensors although they are initially isotropic. Furthermore, we identify numerical stability of the developed sequential method from the test cases that exhibit the highly complex coupled gas hydrate systems with large deformation. Thus, the proposed sequential formulation can be applied in largely deformable gas hydrate systems.

42 ENGINEERING↗

DOE OSTI2018

Multi-level spectral deferred corrections scheme for the shallow water equations on the rotating sphere

Efficient time integration schemes are necessary to capture the complex processes involved in atmospheric flows over long periods of time. We propose a high-order, implicit–explicit numerical scheme that combines Multi-Level Spectral Deferred Corrections (MLSDC) and the Spherical Harmonics (SH) transform to solve the wave-propagation problems arising from the shallow-water equations on the rotating sphere. The iterative temporal integration is based on a sequence of corrections distributed on coupled space–time levels to perform a significant portion of the calculations on a coarse representation of the problem and hence to reduce the time-to-solution while preserving accuracy. In our scheme, referred to as MLSDC-SH, the spatial discretization plays a key role in the efficiency of MLSDC, since the SH basis allows for consistent transfer functions between space–time levels that preserve important physical properties of the solution. We study the performance of the MLSDC-SH scheme with shallow-water test cases commonly used in numerical atmospheric modeling. We use this suite of test cases, which gradually adds more complexity to the nonlinear system of governing partial differential equations, to perform a detailed analysis of the accuracy of MLSDC-SH upon refinement in time. We illustrate the stability properties of MLSDC-SH and show that the proposed scheme achieves up to eighth-order convergence in time. Finally, we study the conditions in which MLSDC-SH achieves its theoretical speedup, and we show that it can significantly reduce the computational cost compared to single-level Spectral Deferred Corrections (SDC).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Effects of Central Cut Width on the Dynamical Characteristics of Box Assembly Structure

An investigation into the Box Assembly with Removable Component (BARC) structure is conducted by utilizing computational simulations and experimental structural testing in order to determine the complex dynamical responses instigated by the central cut of the system. Because the dynamics of the BARC system is complex, this study focuses primarily on analyzing the behavior of the box assembly (BA) system. The investigation explores the dynamics of the BA system by varying the central cut widths, ranging from a cut as wide as 0.5” cut to a 0.25” cut system, as well as a 0.1” cut and a system with no cut at all. Experimental testing is performed on each system including a free vibration test using an impact hammer to excite and identify the dominant frequencies of each structure. This testing is followed by pseudo-random vibration tests and swept sinusoidal excitation tests to determine the nonlinear aspects of these systems, such as the possible existence of nonlinear softening, hardening, and/or damping. The results show that nonlinear softening and nonlinear damping are present in each system. The no-cut system demonstrated the highest peak frequencies throughout all the tests, being the most rigid structure. The 0.25” cut system was shown to have the highest peak frequencies among all the cut systems in both the finite elemenet analysis (FEA) and impact testing. This trend did not continue, though, in the random and harmonic testing, possibly due to the added stiffness of the test setup with the slip table and stinger. The results show the importance of accurately measuring the central cut width and how possible geometric uncertainties change the overall dynamical behaviors of complex systems, such as natural characteristics, nonlinear responses, coupling of modes, and oscillating amplitudes.

Padilla, Christopher (ORCID:000900033446732X)↗

DOE OSTI2020

Simulation of coupled multiphase flow and geomechanics in porous media with embedded discrete fractures

In fractured natural formations, the equations governing fluid flow and geomechanics are strongly coupled. Hydrodynamical properties depend on the mechanical configuration, and they are therefore difficult to accurately resolve using uncoupled methods. In recent years, significant research has focused on discretization strategies for these coupled systems, particularly in the presence of complicated fracture network geometries. In this work, we explore a finite-volume discretization for the multiphase flow equations coupled with a finite-element scheme for the mechanical equations. Fractures are treated as lower dimensional surfaces embedded in a background grid. Interactions are captured using the embedded discrete fracture model (EDFM) and the embedded finite element method (EFEM) for the flow and the mechanics, respectively. This nonconforming approach significantly alleviates meshing challenges. EDFM considers fractures as lower dimension finite volumes that exchange fluxes with the rock matrix cells. The EFEM method provides, instead, a local enrichment of the finite-element space inside each matrix cell cut by a fracture element. Both the use of piecewise constant and piecewise linear enrichments are investigated. They are also compared to an extended finite element approach. One key advantage of EFEM is the element-based nature of the enrichment, which reduces the geometric complexity of the implementation and leads to linear systems with advantageous properties. Synthetic numerical tests are presented to study the convergence and accuracy of the proposed method. It is also applied to a realistic scenario, involving a heterogeneous reservoir with a complex fracture distribution, to demonstrate its relevance for field applications.

58 GEOSCIENCES↗

DOE OSTI2022

Simulation of the High Temperature Test Facility (HTTF) Core Using the 2D Ring Model with SAM

A two-dimensional ring model is developed with SAM to model the core of the High Temperature Test Facility (HTTF) at the system level. The ring model simplifies the complex structure of the HTTF core by converting the hexagonal rows of heaters and flow channels into layers of concentric annular rings. The ring model is first compared against a 3D-1D model where the solid structures are fully resolved in three dimensions while the fluid structures are modeled as one-dimensional flows. Comparison between the 3D-1D and the ring models shows that the latter can predict major parameters reasonably well under steady-state normal operating condition, but the heater temperatures are underpredicted. Adjustment is made to the effective thermal conductivity of the ceramic core of the ring model to improve the heater temperature predictions. Furthermore, the ring model is also used to simulate a transient Pressurized Conduction Cooldown (PCC) condition and is benchmarked with the experimental data from the HTTF Test PG-27. Good agreement is obtained between the experimental data and the predictions by the ring model.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2022

What can simulation test beds teach us about social science? Results of the ground truth program

The ground truth program used simulations as test beds for social science research methods. The simulations had known ground truth and were capable of producing large amounts of data. This allowed research teams to run experiments and ask questions of these simulations similar to social scientists studying real-world systems, and enabled robust evaluation of their causal inference, prediction, and prescription capabilities. We tested three hypotheses about research effectiveness using data from the ground truth program, specifically looking at the influence of complexity, causal understanding, and data collection on performance. We found some evidence that system complexity and causal understanding influenced research performance, but no evidence that data availability contributed. The ground truth program may be the first robust coupling of simulation test beds with an experimental framework capable of teasing out factors that determine the success of social science research.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Overview of the Systems Engineering Process as It Applies to The National Spherical Torus Experiment - Upgrade (NSTX-U)

This paper addresses the systems engineering (SE) processes used for the National Spherical Torus Experiment-Upgrade (NSTX-U). It focuses on SE across the life cycle of the system, including requirements management, interface control, risk management, integration, and verification/validation. This is particularly significant as NSTX-U includes new systems and an existing plant and reused systems from past projects such as the Tokamak Fusion Test Reactor (TFTR). The implementation of SE provides the ability to control complexity, improve communications, identify risks early, and prevent defects. Systems engineering principles are applied to enhance the integration while maintaining relevance in plasma research. Furthermore, these principles define a deliberate process to identify and resolve issues early in the development cycle, thus reducing risks and optimizing outputs. They also establish relationships to gather knowledge from experts and stakeholders, supporting the continued ability of NSTX-U in building and maintaining an operational system able to adapt to changing environments and emerging requirements.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Exploration of multifidelity UQ sampling strategies for computer network applications.

Network modeling is a powerful tool to enable rapid analysis of complex systems that can be challenging to study directly using physical testing. Here, two approaches are considered: emulation and simulation. The former runs real software on virtualized hardware, while the latter mimics the behavior of network components and their interactions in software. Although emulation provides an accurate representation of physical networks, this approach alone cannot guarantee the characterization of the system under realistic operative conditions. Operative conditions for physical networks are often characterized by intrinsic variability (payload size, packet latency, etc.) or a lack of precise knowledge regarding the network configuration (bandwidth, delays, etc.); therefore uncertainty quantification (UQ) strategies should be also employed. UQ strategies require multiple evaluations of the system with a number of evaluation instances that roughly increases with the problem dimensionality, i.e., the number of uncertain parameters. It follows that a typical UQ workflow for network modeling based on emulation can easily become unattainable due to its prohibitive computational cost. In this paper, a multifidelity sampling approach is discussed and applied to network modeling problems. The main idea is to optimally fuse information coming from simulations, which are a low-fidelity version of the emulation problem of interest, in order to decrease the estimator variance. By reducing the estimator variance in a sampling approach it is usually possible to obtain more reliable statistics and therefore a more reliable system characterization. Several network problems of increasing difficulty are presented. For each of them, the performance of the multifidelity estimator is compared with respect to the single fidelity counterpart, namely, Monte Carlo sampling. For all the test problems studied in this work, the multifidelity estimator demonstrated an increased efficiency with respect to MC.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

The Digital Engineering Vision for DOME: Facilitating Design, Deployment, and Operations [Poster]

DOME is a planned microreactor test facility at INL’s Materials and Fuels Complex. It is a complex system with several interdependent sub-systems such as the reactor (up to 20 MWth), radioactive confinement, temperature and pressure regulation system, ventilation system, etc. The engineering design process for such a system traditionally involves several documents from various sources and the system information is scattered across these documents. Digital engineering represents a paradigm shift through which systems are designed using digital models and integrated data. The digital engineering vision for DOME utilizes a model-based systems engineering (MBSE) approach. The system architecture, physical components, control logic, and verification experiments are all designed using MathWorks MATLAB and Simulink. This hierarchical model can combine data from multiple sources at various levels of abstraction. It can be used to simulate the facility’s operations and to test the system using different sets of parameters. Its capabilities can be expanded by interfacing it with high-fidelity multi-physics models, risk analysis tools, etc. The same model can evolve into a digital twin that can monitor operations and conduct predictive analysis using real-time sensor data from the facility. The eventual goal of this effort is to transform the end-to-end engineering of nuclear facilities in every phase of their lifecycle, including design, deployment, and operations.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2024

SinhaRoy_TechPresentation_2024 [Slides]

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2023

Single-Point Extrapolation to the Complete Basis Set Limit through Deep Learning

Machine learning (ML) offers an attractive method for making predictions about molecular systems while circumventing the need to run expensive electronic structure calculations. Once trained on ab initio data, the promise of ML is to deliver accurate predictions of molecular properties that were previously computationally infeasible. In this work, we develop and train a graph neural network model to correct the basis set incompleteness error (BSIE) between a small and large basis set at the RHF and B3LYP levels of theory. Our results show that, when compared to fitting to the total potential, an ML model fitted to correct the BSIE is better at generalizing to systems not seen during training. We test this ability by training on single molecules while evaluating on molecular complexes. We also show that ensemble models yield better behaved potentials in situations where the training data is insufficient. However, even when only fitting to the BSIE, acceptable performance is only achieved when the training data sufficiently resemble the systems one wants to make predictions on. As a result, the test error of the final model trained to predict the difference between the cc-pVDZ and cc-pV5Z potential is 0.184 kcal/mol for the B3LYP density functional, and the ensemble model accurately reproduces the large basis set interaction energy curves on the S66x8 dataset.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Real-time Data Analytics for Condition Monitoring of Complex Industrial Systems

Modern industrial systems are now fitted with several sensors for condition monitoring. This is advantageous because these sensors can provide mass amounts of data that have the potential for aiding in tasks such as fault detection, diagnosis, and prognostics. However, the information valuable for performing these tasks is often clouded in noise and must be mined from high-dimensional data structures. Therefore, this dissertation presents a data analytics framework for performing these condition monitoring tasks using high-dimensional data. Demonstrations of this framework are detailed for challenges related to power generation systems in automobiles, power plants, and aircraft engines. These implementations leverage data collected from state-of-the-art, industry class test-rigs. Results indicate the ability of this framework to develop effective methodologies for condition monitoring of complex systems.

Peters, Benjamin↗

DOE OSTI2017

Overview of the preliminary design of the ITER plasma control system

An overview of the Preliminary Design of the ITER Plasma Control System (PCS) is described here, which focusses on the needs for 1st plasma and early plasma operation in hydrogen/helium (H/He) up to a plasma current of 15 MA with moderate auxiliary heating power in low confinement mode (L-mode). Candidate control schemes for basic magnetic control, including divertor operation and kinetic control of the electron density with gas puffing and pellet injection, were developed. Commissioning of the auxiliary heating systems is included as well as support functions for stray field topology and real-time plasma boundary reconstruction. Initial exception handling schemes for faults of essential plant systems and for disruption protection were developed. The PCS architecture was also developed to be capable of handling basic control for early commissioning and the advanced control functions that will be needed for future high performance operation. A plasma control simulator is also being developed to test and validate control schemes. To handle the complexity of the ITER PCS, a systems engineering approach has been adopted with the development of a plasma control database to keep track of all control requirements.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

A windowed mean trajectory approximation for condensed phase dynamics

We propose a trajectory-based quasi-classical method for approximating dynamics in condensed phase systems. Building upon the previously developed optimized mean trajectory approximation that has been used to compute linear and nonlinear spectra, we borrow some ideas from filtering trajectory methods to obtain a novel semiclassical method for the dynamical propagation of density matrices. This new approximation is tested rigorously against standard multistate electronic models, spin-boson models, and models of the Fenna–Matthews–Olson complex. For dissipative systems, the current method is significantly better or as good as many other semiclassical methods available, especially at low temperatures and for off-diagonal density matrix elements, whereas for scattering models, the current method bears similar limitations as mean-field propagation schemes. All results are tested against the numerically exact hierarchical equations of motion method. In conclusion, the new method shows excellent agreement across various parameter regimes with numerically exact results, highlighting the robustness and accuracy of our approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Acid–base concentration swing for direct air capture of carbon dioxide

This work demonstrates the first experimental evidence of the acid–base concentration swing (ABCS) for direct air capture of CO 2 . This process is based on the effect that concentrating particular acid–base chemical reactants will strongly acidify solution, through Le Chatelier's principle, and result in outgassing absorbed CO 2 . After collecting the outgassed CO 2 , diluting the solution will result in a reversal of the acid–base reaction, basifying the solution and allowing for atmospheric CO 2 absorption. The experimental study examines a system that includes sodium cation as the alkalinity carrier, boric acid, and a polyol complexing agent that reversibly reacts with boric acid to strongly acidify solution upon concentration. Though the tested experimental system faces absorption rate and water capacity limitations, the ABCS process described here provides a basis for further process optimization. A generalized theoretical ABCS reaction framework is developed and different reaction orders and conditions are studied mathematically. Higher order reactions yield favorable cycle output results, reaching volumetric cycle capacity above 50 mM for third-order and 80 mM for fourth-order reactions. Optimal equilibrium constants are determined in order to guide alternative chemical searches and synthetic chemistry design targets. There is a substantial energetic benefit for reaction orders above the first, with second- and third-order ABCS cycles exhibiting a thermodynamic minimum work for the concentrating and outgassing steps around 150 kJ per mole of CO 2 . A significant advantage of the ABCS is that it can be driven through well-developed and widely-deployed desalination technologies, such as reverse osmosis, with opportunities for energy recovery when recombining the concentrated and diluted streams, and extraction can occur directly from the liquid phase upon vacuum application.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Tunable and Robust Optical and Structural Properties of a Cooperative Squaraine-Dye Aggregate-DNA DX-DAE Tile System

Molecular excitons, which are excitations delocalized over multiple dyes in a wavelike manner, are of interest for a wide range of applications, including quantum information science. Numerous studies have templated a variety of synthetic dyes via a DNA scaffold to induce dye aggregation to create molecular excitons upon photoexcitation. Dye aggregate optical properties are critically dependent on relative dye geometry and local environment; therefore, an understanding of dye-dye and DNA-dye interactions is critical for advancing toward more complex DNA-dye systems. The extensively studied DNA Holliday junction (HJ) and less-studied double-crossover (DX) tile motif are fundamental test beds for designing complex and ultimately modular DNA-dye architectures. Here, we report the first study of single-linked squaraine dye aggregation and exciton delocalization on a larger and more stable (compared with the HJ) DX tile motif. We first highlight a few DNA-dye constructs that support single dyes and aggregates with distinct optical properties that are both tunable—through sample design, buffer conditions, and heat treatment—and robust to environment changes, including transfer to solid phase. Next, we assess several experimental and design considerations that demonstrate directed dye-driven assembly of a novel double-tile DNA configuration. Our results demonstrate that single-linked squaraine dyes templated to DX tiles provide a viable research path to design and evaluate dye aggregate networks that support exciton delocalization. We include herein the first report of exciton delocalization in the solid phase in a DNA-dye construct. Additionally, our findings indicate that dye aggregation impacts the assembly of the DNA-dye construct, and, in some cases, thereby cooperates with the DNA to determine a final robust system configuration. Finally, we show that a controlled annealing schedule can be employed to promote the homogeneous assembly of DNA-dye constructs. The findings in this study contribute to the understanding of DNA-dye systems and the relevant factors involved in their directed assembly to achieve specific constructs with desirable properties.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Deep reinforcement learning control for co-optimizing energy consumption, thermal comfort, and indoor air quality in an office building

With the recent demand for decarbonization and energy efficiency, advanced HVAC control using Deep Reinforcement Learning (DRL) becomes a promising solution. Due to its flexible structures, DRL has been successful in energy reduction for many HVAC systems. However, only a few researches applied DRL agents to manage the entire central HVAC system and control multiple components in both the water loop and the air loop, owing to its complex system structures. Moreover, those researches have not extended their applications by incorporating the indoor air quality, especially both CO2 and PM2.5concentrations, on top of energy saving and thermal comfort, as achieving those objectives simultaneously can cause multiple control conflicts. What's more, DRL agents are usually trained on the simulation environment before deployment, so another challenge is to develop an accurate but relatively simple simulator. Therefore, we propose a DRL algorithm for a central HVAC system to co-optimize energy consumption, thermal comfort, indoor CO2 level, and indoor PM2.5 level in an office building. To train the controller, we also developed a hybrid simulator that decoupled the complex system into multiple simulation models, which are calibrated separately using laboratory test data. The hybrid simulator combined the dynamics of the HVAC system, the building envelope, as well as moisture, CO2, and particulate matter transfer. Three control algorithms (rule-based, MPC, and DRL) are developed, and their performances are evaluated on the hybrid simulator environment with a realistic scenario (i.e., with stochastic noises). The test results showed that, the DRL controller can save 21.4 % of energy compared to a rule-based controller, and has improved thermal comfort, reduced indoor CO2 concentration. The MPC controller showed an 18.6 % energy saving compared to the DRL controller, mainly due to savings from comfort and indoor air quality boundary violations caused by unmeasured disturbances, and it also highlights computational challenges in real-time control due to non-linear optimization. Finally, we provide the practical considerations for designing and implementing the DRL and MPC controllers based on their respective pros and cons.

Guo, Fangzhou↗