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DOE OSTI2024

Physics-Informed Active Learning With Simultaneous Weak-Form Latent Space Dynamics Identification

The parametric greedy latent space dynamics identification (gLaSDI) framework has demonstrated promising potential for accurate and efficient modeling of high-dimensional nonlinear physical systems. However, it remains challenging to handle noisy data. Here, to enhance robustness against noise, we incorporate the weak-form estimation of nonlinear dynamics (WENDy) into gLaSDI. In the proposed weak-form gLaSDI (WgLaSDI) framework, an autoencoder and WENDy are trained simultaneously to discover intrinsic nonlinear latent-space dynamics of high-dimensional data. Compared with the standard sparse identification of nonlinear dynamics (SINDy) employed in gLaSDI, WENDy enables variance reduction and robust latent space discovery, therefore leading to more accurate and efficient reduced-order modeling. Furthermore, the greedy physics-informed active learning in WgLaSDI enables adaptive sampling of optimal training data on the fly for enhanced modeling accuracy. The effectiveness of the proposed framework is demonstrated by modeling various nonlinear dynamical problems, including viscous and inviscid Burgers' equations, time-dependent radial advection, and the Vlasov equation for plasma physics. With data that contains 5%–10% Gaussian white noise, WgLaSDI outperforms gLaSDI by orders of magnitude, achieving 1%–7% relative errors. Compared with the high-fidelity models, WgLaSDI achieves 121 to 1779x speed-up.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Redox poise in R. rubrum phototrophic growth drives large-scale changes in macromolecular pathways

During photoheterotrophic growth on organic substrates, purple nonsulfur photosynthetic bacteria like Rhodospirillum rubrum can acquire electrons by multiple means, including oxidation of organic substrates, oxidation of inorganic electron donors (e.g., H 2 ), and by reverse electron flow from the photosynthetic electron transport chain. These electrons are stored as reduced electron-carrying cofactors (e.g., NAD(P)H and ferredoxin). The overall ratio of oxidized to reduced cofactors (e.g., NAD(P)+:NAD(P)H), or ’redox poise’, is difficult to understand or predict, as are the cellular processes for dissipating these reducing equivalents. Using physics-based models that capture mass action kinetics consistent with the thermodynamics of reactions and pathways, a range of redox conditions for heterophototrophic growth are evaluated, from conditions in which the NADP+/NADPH levels approach thermodynamic equilibrium to conditions in which the NADP+/NADPH ratio is far above the typical physiological values. Modeling predictions together with experimental measurements indicate that the redox poise of the cell results in large-scale changes in the activity of biosynthetic pathways and, thus, changes in cell macromolecule levels (DNA, RNA, proteins, and fatty acids). Furthermore, modeling predictions indicate that during phototrophic growth, reverse electron flow from the quinone pool is a minor contributor to the production of reduced cofactors (e.g., NAD(P)H) compared to other oxidative processes (H 2 and carbon substrate oxidation). Instead, the quinone pool primarily operates to aid ATP production. The high level of ATP, in turn, drives reduction processes even when NADPH levels are relatively low compared to NADP+ by coupling ATP hydrolysis to the reductive processes. The model, in agreement with experimental measurements of macromolecule ratios of cells growing on different carbon substrates, indicates that the dynamics of nucleotide versus lipid and protein production is likely a significant mechanism of balancing oxidation and reduction in the cell.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Weak-Form Latent Space Dynamics Identification

This software showcases the enhanced capabilities of the Latent Space Dynamics Identification (LaSDI) algorithm through the application of the weak form, resulting in WLaSDI. WLaSDI first compresses the data, then projects it onto test functions, and subsequently learns the local latent space models. Notably, WLaSDI demonstrates significantly improved robustness to noise. Using weak-form equation learning techniques, WLaSDI achieves local latent space modeling. Compared to the standard sparse identification of nonlinear dynamics (SINDy) used in LaSDI, the variance reduction of the weak form ensures robust and precise latent space recovery, enabling fast, robust, and accurate simulations. We demonstrate the efficacy of WLaSDI against LaSDI using several common benchmark examples, including viscid and inviscid Burgers', radial advection, and heat conduction. For instance, in 1D inviscid Burgers' simulations with up to 100% Gaussian white noise, WLaSDI maintains relative errors consistently below 6%, whereas LaSDI errors can exceed 10,000%. Similarly, in radial advection simulations, WLaSDI keeps relative errors below 16%, compared to potential errors of up to 10,000% with LaSDI. Additionally, WLaSDI achieves significant speedups, such as a 140X speedup in 1D Burgers' simulations compared to the corresponding full order model.

Choi, Youngsoo↗

DOE OSTI2021

Nonlinear Interface Reduction for Time-Domain Analysis of Hurty/Craig-Bampton Superelements with Frictional Contact

Virtual prototyping in engineering design relies today on modern numerical models of contacting structures with accurate resolution of interface mechanics, which strongly affect the system-level stiffness and energy dissipation due to frictional losses. High-fidelity modeling within the localized interfaces is required to resolve local quantities of interest that may drive design decisions. The high-resolution finite element meshes necessary to resolve inter-component stresses tend to be computationally expensive, particularly when the analyst is interested in response time histories. The Hurty/Craig-Bampton (HCB) transformation is a widely used method in structural dynamics for reducing the interior portion of a finite element model while having the ability to retain all nonlinear contact degrees of freedom (DOF) in physical coordinates. These models may still require many DOF to adequately resolve the kinematics of the interface, leading to inadequate reduction and computational savings. This study proposes a novel interface reduction method to overcome these challenges by means of system-level characteristic constraint (SCC) modes and properly orthogonal interface modal derivatives (POIMDs) for transient dynamic analyses. Both SCC modes and POIMDs are computed using the reduced HCB mass and stiffness matrices, which can be directly computed from many commercial finite element analysis software. Comparison of time history responses to an impulse-type load in a mechanical beam assembly indicate that the interface-reduced model correlates well with the HCB truth model. Localized features like slip and contact area are well-represented in the time domain when the beam assembly is loaded with a broadband excitation. The proposed method also yields reduced-order models with greater critical timestep lengths for explicit integration schemes.

42 ENGINEERING↗

DOE OSTI2020

A cavitation and dynamic void growth model for a general class of strain-softening amorphous materials

In this work, we derive a homogenized framework for cavitation and dynamic void growth in a general class of strain-softening materials with particular emphasis on amorphous materials. Analytic solutions are derived by considering an assemblage of spherical shells subject to dynamic hydrostatic tensile pressure. The isochoric response of the matrix material is captured by a free volume theory based amorphous viscoplasticity model. The framework accounts for the coupled rate-dependent, strain-softening behavior typically exhibited in amorphous materials. Validation of the homogenized theory is carried out against numerous direct numerical simulations with excellent agreement. Furthermore, we find that a reduction in cavitation strength and significant acceleration of dynamic void growth rates is induced as a consequence of strain-softening in the amorphous matrix material. Lastly, the model is utilized to interpret some non-intuitive experimental observations of amorphous materials subject to shock compression and subsequent spall failure.

36 MATERIALS SCIENCE↗

DOE OSTI2020

The Adjoint Petrov–Galerkin method for non-linear model reduction

Here, we formulate a new projection-based reduced-order modeling technique for non-linear dynamical systems. The proposed technique, which we refer to as the Adjoint Petrov–Galerkin (APG) method, is derived by decomposing the generalized coordinates of a dynamical system into a resolved coarse-scale set and an unresolved fine-scale set. A Markovian finite memory assumption within the Mori–Zwanzig formalism is then used to develop a reduced-order representation of the coarse scales. This procedure leads to a closed reduced-order model that displays commonalities with the adjoint stabilization method used in finite elements. The formulation is shown to be equivalent to a Petrov–Galerkin method with a non-linear, time-varying test basis, thus sharing some similarities with the Least-Squares Petrov–Galerkin method. Theoretical analysis examining a priori error bounds and computational cost is presented. Numerical experiments on the compressible Navier–Stokes equations demonstrate that the proposed method can lead to improvements in numerical accuracy, robustness, and computational efficiency over the Galerkin method on problems of practical interest. Improvements in numerical accuracy and computational efficiency over the Least-Squares Petrov–Galerkin method are observed in most cases.

42 ENGINEERING↗

DOE OSTI2025

A dynamic protein interactome drives energy conservation and electron flux in Thermococcus kodakarensis

ABSTRACT Life is supported by energy gains fueled by catabolism of a wide range of substrates, each reliant on the selective partitioning of electrons through redox ( red uction and ox idation) reactions. Electron flux through tunable and regulated protein interactions provides dynamic routes for energy conservation, but how electron flux is regulated in vivo , particularly for archaeal metabolisms that support rapid growth at the thermodynamic limits of life, is poorly understood. Identification of bona fide in vivo protein assemblies and how such assemblies dictate the totality of electron flux is critical to our understanding of the regulation imposed on metabolism, energy production, and energy conservation. Here, 25 key proteins in central metabolic redox pathways in the model, genetically accessible, hyperthermophilic archaeon Thermococcus kodakarensis , were purified to reveal an extensive, dynamic, and tightly interconnected network of protein interactions that responds to environmental cues (such as the availability of various reductive sinks) to direct electron flux to maximize energetic gains. Interactions connecting disparate functions suggest many catabolic and anabolic activities occur in spatial proximity in vivo , and while protein complexes have been historically defined under optimal conditions, many of these complexes appear to maintain alternative partnerships in changing conditions. The totality of the results obtained redefines our understanding of in vivo assemblies driving ancient metabolic strategies supporting the growth of modern Archaea. IMPORTANCE Given the potential for rational genetic manipulations of biofuel- and biotech-promising archaea to yield transformative results for major markets, it is a priority to define how the metabolisms of such species are controlled, at least in part, by in vivo protein assemblies, and from such, define routes of energy flux that can be most efficiently altered toward biofuel or biotechnological gains. Proteinaceous electron carriers (PECs, such as ferredoxins) offer the potential for specific protein–protein interactions to coordinate selective reductive flow. Employing the model, genetically accessible, hyperthermophilic archaeon, Thermococcus kodakarensis , we establish the metabolic protein interactome of 25 key redox proteins, revealing that each redox active protein has a dynamic partnership profile, suggesting catabolic and anabolic activities may occur in concert and in temporal and spatial proximity in vivo . These results reveal critical importance in evaluating the newly identified partnerships and their role and utility in providing regulated redox flux in T. kodakarensis .

Williams, Sere A. (ORCID:0000000235509590)↗

DOE OSTI2025

FPGA-accelerated SpeckleNN with SNL for real-time X-ray single-particle imaging

We present the implementation of a specialized version of our previously published unified embedding model, SpeckleNN, for real-time speckle pattern classification in X-ray Single-Particle Imaging (SPI), using the SLAC Neural Network Library (SNL) on an FPGA platform. This hardware realization transitions SpeckleNN from a prototypic model into a practical edge solution, optimized for running inference near the detector in high-throughput X-ray free-electron laser (XFEL) facilities, such as those found at the Linac Coherent Light Source (LCLS). To address the resource constraints inherent in FPGAs, we developed a more specialized version of SpeckleNN. The original model, which was designed for broader classification across multiple biological samples, comprised ~5.6 million parameters. The new implementation, while reducing the parameter count to 64.6K (a 98.8% reduction), focuses on maintaining the model's essential functionality for real-time operation, achieving an accuracy of 90%. Furthermore, we compressed the latent space from 128 to 50 dimensions. This implementation was demonstrated on the KCU1500 FPGA board, utilizing 71% of available DSPs, 75% of LUTs, and 48% of FFs, with an average power consumption of 9.4W according to the Vivado post-implementation report. The FPGA performed inference on a single image with a latency of 45.015 microseconds at a 200 MHz clock rate. In comparison, running the same inference on an NVIDIA A100 GPU resulted in an average power consumption of ~73W and an image processing latency of around 400 microseconds. Our FPGA-accelerated version of SpeckleNN demonstrated significant improvements, achieving an 8.9 × speedup and a 7.8 × reduction in power consumption compared to the GPU implementation. Key advancements include model specialization and dynamic weight loading through SNL, which eliminates the need for time-consuming FPGA design re-synthesis, allowing fast and continuous deployment of models (re)trained online. These innovations enable real-time adaptive classification and efficient vetoing of speckle patterns, making SpeckleNN more suited for deployment in XFEL facilities. This implementation has the potential to significantly accelerate SPI experiments and enhance adaptability to evolving experimental conditions.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Development of A Multi-Spectral Pyrometry Sensor for High-Speed Transient Surface-Temperature Measurements in Combustion-Relevant Harsh Environments

Accurate and high-speed transient surface-temperature measurements of combustion devices including internal combustion (IC) engines, gas turbines, etc., provide validation targets and boundary conditions for computational fluid dynamics models, and are broadly relevant to technology advancements such as performance improvement and emissions reduction. Development and demonstration of a multi-infrared-channel pyrometry-based optical instrument for high-speed surface-temperature measurement is described. The measurement principle is based on multi-spectral radiation thermometry (MRT) and uses surface thermal radiation at four discrete spectral regions and a corresponding emissivity model to obtain surface temperature via non-linear least squares (NLLS) optimization. Rules of thumb for specifying the spectral regions and considerations to avoid interference with common combustion products are developed; the impact of these along with linear and non-linear MRT analysis are assessed as a function of temperature and signal-to-noise ratio. A multi-start method to determine the MRT-solution global optimum is described and demonstrated. The resulting multi-channel transient pyrometry instrument is described along with practical considerations including optical-alignment drift, matching intra-channel transient response, and solution-confidence indicators. The instrument demonstrated excellent >97% accuracy and >99% 2-sigma precision over the 400–800 °C range, with ~20 µs (50 kHz, equivalent to 0.2 cad at 2000 RPM IC-engine operation) transient response in the bench validation.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Modeling and Analysis of a Heat Pump Clothes Dryer with Thermal Energy Storage

Clothes drying is an energy-intensive process that causes significant electricity consumption and carbon emissions in the US. Approximately 83% of Households in the US own a tumble clothes dryer at home and 80% of dryers are electrical resistance dryers with low energy efficiency. Heat pump technology makes it possible for highly efficient and clean drying. Additionally, the ventless design of heat pump clothes dryers (HPCD) provides more installation flexibility. HPCD involves three primary mediums: wet clothes, a closed air loop, and a refrigerant circuit. The evaporator is used to dehumidify the wet air and the condenser is used to re-heat the dry air. One of the critical technological barriers to HPCD market penetration is its long drying time, primarily due to the relatively low discharging temperature and the slow response during the warm-up period. In this study, the thermal energy storage (TES) technology is adopted to address this challenge by providing pre-heating of air prior to the condenser to increase the operating temperature of the process air. The heat pump will charge the phase change material (PCM) in the TES device with heating energy during clothes washing and the PCM will discharge the stored heat to facilitate air heating during clothes drying. To analyze the optimal design and potential for energy saving and drying time reduction, a mathematical model of the HPCD system was developed. The HPCD is a highly dynamic system with a coupled heat and mass transfer and heat pumping cycle. This paper provides solutions to simulate the transient behavior of the system while maintaining low computational cost. The modeling result indicates reduced energy consumption and drying time by integrating TES with HPCD, as compared to electrical resistance dryers. The study can provide significant insights into improving building flexibility with TES and smart appliances.

Liu, Xiaoli↗

DOE OSTI2025

Atomically Revealing Bulk Point Defect Dynamics in Hydrogen‐Driven γ‐Fe 2 O 3 → Fe 3 O 4 → FeO Transformation

Understanding how point defects in the bulk govern redox transformations is essential for advancing hydrogen-based metal production and designing high-performance oxide materials. This study reveals the atomic-scale mechanisms driving hydrogen-induced reduction of γ-Fe 2 O 3 to Fe 3 O 4 , focusing on how bulk vacancy dynamics dictate structural evolution and reaction kinetics. A key finding is the pronounced contrast in defect behavior between the two oxides: in γ-Fe 2 O 3 , intrinsic Fe vacancies promote oxygen vacancy clustering, destabilizing the local lattice and driving nanopore formation. In contrast, Fe 3 O 4 exhibits a higher oxygen vacancy formation energy and lacks intrinsic Fe vacancies, suppressing vacancy aggregation and maintaining a dense, pore-free structure. This divergence governs distinct reduction pathways—γ-Fe 2 O 3 undergoes an interface-reaction-limited transformation confined to the γ-Fe 2 O 3 /Fe 3 O 4 boundary, while Fe 3 O 4 supports a uniform increase in oxygen vacancy concentration, enabling bulk-phase reduction to lower-oxide FeO. Integrated in situ electron microscopy and density functional theory modeling uncover a vacancy-mediated mechanism, where synergistic cation-anion vacancy dynamics steer microstructure evolution and phase progression. These insights highlight the critical role of vacancy dynamics in controlling oxide reactivity and offer a pathway toward vacancy engineering to enhance reduction kinetics in hydrogen metallurgy and to tailor porosity, reactivity, and structural resilience in oxide-based catalysts and energy materials.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Flow reduction of hydrocarbon liquid in silica nanochannel: Insight from many-body dissipative particle dynamics simulations

A modified many-body dissipative particle dynamics (mDPD) model recently developed for realistic mesoscale multiphase flow simulations is rigorously parameterized, calibrated, and applied for elucidating the flow mechanisms of hydrocarbon liquids (i.e., heptane in this work) in amorphous silica cylindrical nanochannels with inner diameters ranging from 4.5 to 22.5 nm. The simulation results suggest the presence of a strong threshold of pressure gradient under which heptane cannot be driven to flow. The threshold for the 4.5 nm diameter pore is 10 to 100 times as high as for the 9–22.5 nm diameter pore, highlighting a remarkable nanoconfinement effect. Fluid viscosity is found to exhibit a shear-thinning phenomenon with intensity to weaken with increasing channel diameter — a phenomenon not observed in nanochannel flow of liquid water and gas in literature. Most remarkably, the radial profiles of average longitudinal flow velocity fitted by the modified Hagen-Poiseuille equation showed a negative slip length (–2.5% to –0.5% relative to the diameter) and a reduction of apparent permeability by 16% to 23%. Furthermore, this finding suggests silica nanochannels tend to deter hydrocarbon flow, a phenomenon that is opposed to the flow enhancement reported in most of the prior nanochannel flow studies in literature.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

Cluster dynamics modeling of irradiation growth in single crystal Zr

Irradiation growth of single-crystal Zr is modeled with a reduced set of cluster dynamics equations. Nucleation and growth of basal and prismatic dislocation loops are both accounted for in the model. Equations are developed for the time evolution of single point defects, a limited number of point defect clusters, interstitial and vacancy loop nucleation rates, as well as for the growth of vacancy loops on basal planes and interstitial loops on prismatic planes. Reduction of the usual infinite hierarchy of cluster dynamics equations to the simple set studied here is justified on the physical basis of the stability of small loops once nucleated. This simplified cluster dynamics model with a small number of adjustable parameters avoids the complexity of explicit representation of higher order point defect clusters. The model shows consistency with experimental observations of the following aspects: (1) the growth rates of Zr crystals along the a- and c-axes; (2) the onset dose for breakaway irradiation growth; (3) the saturation dislocation loop densities of vacancy and interstitial loops; (4) the effects of cold work and temperature on irradiation growth.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Forward sensitivity analysis and mode dependent control for closure modeling of Galerkin systems

Model reduction by projection-based approaches is often associated with losing some of the important features that contribute towards the dynamics of the retained scales. As a result, a mismatch occurs between the predicted trajectories of the original system and the truncated one. We put forth a framework to apply a continuous time control signal in the latent space of the reduced order model (ROM) to account for the effect of truncation. We set the control input using parameterized models by following energy transfer principles. Our methodology relies on observing the system behavior in the physical space and using the projection operator to restrict the feedback signal into the latent space. Then, we leverage the forward sensitivity method (FSM) to derive relationships between the feedback and the desired mode-dependent control. We test the performance of the proposed approach using two test cases, corresponding to viscous Burgers and vortex merger problems at high Reynolds number. Results show that the ROM trajectory with the applied FSM control closely matches its target values in both the data-dense and data-sparse regimes.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Understanding latent timescales in neural ordinary differential equation models of advection-dominated dynamical systems

The neural ordinary differential equation (ODE) framework has shown considerable promise in recent years in developing highly accelerated surrogate models for complex physical systems characterized by partial differential equations (PDEs). For PDE-based systems, state-of-the-art neural ODE strategies leverage a two-step procedure to achieve this acceleration: a nonlinear dimensionality reduction step provided by an autoencoder, and a time integration step provided by a neural-network based model for the resultant latent space dynamics (the neural ODE). This work explores the applicability of such autoencoder-based neural ODE strategies for PDEs in which advection terms play a critical role. More specifically, alongside predictive demonstrations, physical insight into the sources of model acceleration (i.e., how the neural ODE achieves its acceleration) is the scope of the current study. Such investigations are performed by quantifying the effects of both autoencoder and neural ODE components on latent system time-scales using eigenvalue analysis of dynamical system Jacobians. To this end, the sensitivity of various critical training parameters – de-coupled versus end-to-end training, latent space dimensionality, and the role of training trajectory length, for example – to both model accuracy and the discovered latent system timescales is quantified. Furthermore, this work specifically uncovers the key role played by the training trajectory length (the number of rollout steps in the loss function during training) on the latent system timescales: larger trajectory lengths correlate with an increase in limiting neural ODE time-scales, and optimal neural ODEs are found to recover the largest time-scales of the full-order (ground-truth) system. Demonstrations are performed across fundamentally different unsteady fluid dynamics configurations influenced by advection: (1) the Kuramoto–Sivashinsky equations (2) Hydrogen-Air channel detonations (the compressible reacting Navier–Stokes equations with detailed chemistry), and (3) 2D Atmospheric flow.

Advection-dominated dynamical systems↗

DOE OSTI2021

Atomic Origin of the Autocatalytic Reduction of Monoclinic CuO in a Hydrogen Atmosphere

Reducibility is key for the use of bulk metal oxides in chemical transformation involving redox reactions but probing microscopic processes of oxide reduction is challenging. This is because the insulating nature of bulk oxides restricts ion and electron spectroscopic measurements of oxide surfaces. Herein, using a combination of environmental transmission electron microscopy and atomistic modeling, we report direct in-situ atomic-scale observations of the surface and subsurface dynamics and show that the hydrogen induced CuO reduction occurs via the surface decay of Cu-O/Cu bilayer atomic steps, formation of partially reduced CuO superstructure by the self-ordering of O vacancies in the subsurface, and collapse of Cu-O layers in the bulk. In this work, all these substeps can be traced back to the progressively increased concentration and activity of O vacancies in the surface and subsurface of the oxide, thereby leading to the self-accelerated oxide reduction. These results demonstrate the microscopic details that may have broader applicability in modulating various redox processes.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Power System Network Reduction for Power Hardware-in-the-Loop Simulation: Preprint

This paper proposes a single-port equivalent and a two-port equivalent to respectively reduce single-port and two-port areas in a large power network. Parameters of the reduced systems are rigorously derived, which guarantees that the electrical quantities at the port remain unchanged over the reduction, including voltage magnitude and phase, active and reactive power injections into the area to be reduced. The proposed techniques are applied to reduce a practical Maui grid, where the total numbers of buses, lines and transformers are respectively reduced from 212, 106 and 108 to 45, 30 and 13. Dynamic behaviors between the full model and the reduced model are compared in detail to illustrate the efficacy and accuracy of the proposed network reduction.

41 EE - Solar Energy Technologies Office (EE-4S)↗

DOE OSTI2021

Power System Network Reduction for Power Hardware-in-the-Loop Simulation

This paper proposes single-port equivalent and two-port equivalent network reduction methods to respectively reduce single-port and two-port areas in a large power network. Parameters of the reduced systems are rigorously derived, which guarantees that the electrical quantities at the port(s) remain unchanged over the reduction, including voltage magnitude and phase and active and reactive power injections into the area to be reduced. The proposed techniques are applied to reduce a practical Maui grid, where the total numbers of buses, lines and transformers are respectively reduced from 212, 106 and 108 to 45, 30 and 13. Dynamic behaviors between the full model and the reduced model are compared in detail to illustrate the efficacy and accuracy of the proposed network reduction.

model reduction↗