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Metabolic Context Species Interaction Networks (MetConSIN) generates microbe-metabolte and metabolite-metabolite interaction networks using constraint based metabolic modeling. To do this, MetConSIN simulates with the dynamic FBA system and saves the sequence of interaction networks implied by that system, as well as the time-average network.
Next-generation cosmic microwave background (CMB) experiments will have lower noise and therefore increased sensitivity, enabling improved constraints on fundamental physics parameters such as the sum of neutrino masses and the tensor-to-scalar ratio r. Achieving competitive constraints on these parameters requires high signal-to-noise extraction of the projected gravitational potential from the CMB maps. Standard methods for reconstructing the lensing potential employ the quadratic estimator (QE). However, the QE performs suboptimally at the low noise levels expected in upcoming experiments. Other methods, like maximum likelihood estimators (MLE), are under active development. In this work, we demonstrate reconstruction of the CMB lensing potential with deep convolutional neural networks (CNN) - ie, a ResUNet. The network is trained and tested on simulated data, and otherwise has no physical parametrization related to the physical processes of the CMB and gravitati onal lensing. We show that, over a wide range of angular scales, ResUNets recover the input gravitational potential with a higher signal-to-noise ratio than the QE method, reaching levels comparable to analytic approximations of MLE methods. We demonstrate that the network outputs quantifiably different lensing maps when given input CMB maps generated with different cosmologies. We also show we can use the reconstructed lensing map for cosmological parameter estimation. This application of CNN provides a few innovations at the intersection of cosmology and machine learning. First, while training and regressing on images, we predict a continuous-variable field rather than discrete classes. Second, we are able to establish uncertainty measures for the network output that are analogous to standard methods. We expect this approach to excel in capturing hard-to-model non-Gaussian astrophysical foreground and noise contributions.
This paper presents a market-based optimization framework wherein Aggregators can compete for nodal capacity across a distribution feeder and guarantee that allocated flexible capacity cannot cause overloads or congestion. This mechanism, thus, allows Aggregators with allocated capacity to pursue a number of services at the whole-sale market level to maximize revenue of flexible resources. Based on Aggregator bids of capacity (MW) and network access price ($/MW), the distribution system operator (DSO) formulates an optimization problem that prioritizes capacity to the different Aggregators across the network while implicitly considering AC network constraints. This grid-aware allocation is obtained by incorporating a convex inner approximation into the optimization framework that prioritizes hosting capacity to different Aggregators. We adapt concepts from transmission-level capacity market clearing, utility demand charges, and Internet-like bandwidth allocation rules to distribution system operations by incorporating nodal voltage and transformer constraints into the optimization framework. Simulation based results on IEEE distribution networks showcase the effectiveness of the approach.
The effect of bending buckling of carbon nanotubes (CNTs) on thermal conductivity of CNT materials is investigated in atomistic and mesoscopic simulations. Nonequilibrium molecular dynamics simulations of the thermal conductance through an individual buckling kink in a (10,10) single-walled CNT reveal a strong dependence (close to inverse proportionality) of the thermal conductance of the buckling kink on the buckling angle. The value of the buckling kink conductance divided by the cross-sectional area of the CNT ranges from 40 to 10 GWm -2 K -1 as the buckling angle changes from 20 to 110°. The predictions of the atomistic simulations are used for parameterization of a mesoscopic model that enables calculations of thermal conductivity of films composed of thousands of CNTs arranged into continuous networks of bundles. The results of mesoscopic simulations demonstrate that the conductivity of CNT films is sensitive to the angular dependence of the buckling kink conductance and the length of the individual CNTs. For a film composed of 1 $µ$m-long CNTs, the values of the in-plane film conductivity predicted with a constant conductance of 20 GWm -2 K -1 and the angular-dependent conductance obtained in atomistic simulations are about 40 and 20% lower than the conductivity predicted for the same film with zero thermal resistance of the buckling kinks, respectively. The weaker impact of the angular-dependent buckling kink conductance on the effective conductivity of the film is explained by the presence of a large fraction of kinks that have small buckling angles and correspondingly large values of conductance. The results of the simulations suggest that the finite conductance of the buckling kinks has a moderate, but non-negligible, effect on thermal conductivity of materials composed of short CNTs with length up to 1 $µ$m. The contribution of the buckling kink thermal resistance becomes stronger for materials composed of longer CNTs and/or characterized by higher density of buckling kinks.
In this work, we demonstrate SONOS (silicon-oxide-nitrideoxide- silicon) analog memory arrays that are optimized for neural network inference. The devices are fabricated in a 40nm process and operated in the subthreshold regime for in-memory matrix multiplication. Subthreshold operation enables low conductances to be implemented with low error, which matches the typical weight distribution of neural networks, which is heavily skewed toward near-zero values. This leads to high accuracy in the presence of programming errors and process variations. We simulate the end-to-end neural network inference accuracy, accounting for the measured programming error, read noise, and retention loss in a fabricated SONOS array. Evaluated on the ImageNet dataset using ResNet50, the accuracy using a SONOS system is within 2.16% of floating-point accuracy without any retraining. The unique error properties and high On/Off ratio of the SONOS device allow scaling to large arrays without bit slicing, and enable an inference architecture that achieves 20 TOPS/W on ResNet50, a >10× gain in energy efficiency over state-of-the-art digital and analog inference accelerators.
Traffic simulation is an effective tool for urban planners, traffic engineers, and researchers to study traffic. In particular, microscopic traffic simulation, which simulates individual vehicles’ movements within a transportation network, has demonstrated its importance in analyzing and managing transportation systems. However, integrating data from various sources, generating traffic scenarios, and importing information into traffic simulators to conduct microscopic simulations have always been a challenge. This paper presents a solution to overcome this challenge: RealTwin, a comprehensive tool for automated scenario generation for microscopic traffic simulation. Following a streamlined scenario generation and calibration workflow, RealTwin effectively bridges gaps between traffic data from various sources and traffic simulators, making microscopic traffic simulation more accessible for researchers and engineers across various levels of expertise. Using RealTwin to generate a real-world traffic scenario in Simulation of Urban Mobility (SUMO), VISSIM, and AIMSUN, RealTwin’s ability is demonstrated in the construction of realistic and consistent traffic scenarios in different simulators. Furthermore, this paper introduces and illustrates RealTwin’s capability for technology (e.g., autonomous vehicle) scenario generation. This feature can contribute to more comprehensive microscopic simulations, facilitating the analysis of potential effects of various technological innovations on mobility, energy efficiency, and safety. Finally, RealTwin is used to calibrate a simulation in SUMO. In conclusion, the calibration module enhances RealTwin’s ability to generate consistent simulations across different platforms and more realistic simulations that reflect real-world traffic operations.
Numerical simulations of the cardiovascular system are affected by uncertainties arising from a substantial lack of data related to the boundary conditions and the physical parameters of the mathematical models. Quantifying the impact of this uncertainty on the numerical results along the circulatory network is challenged by the complexity of both the morphology of the domain and the local dynamics. Here, we propose to integrate (i) the Transverse Enriched Pipe Element Methods (TEPEM) as a reduced-order model for effectively computing the 3D local hemodynamics; and (ii) a combination of uncertainty quantification via Polynomial Chaos Expansion and classical relaxation methods – called network uncertainty quantification (NetUQ) – for effectively propagating random variables that encode uncertainties throughout the networks. The findings demonstrate the computational effectiveness of computing the propagation of uncertainties in networks with nontrivial topology, including portions of the cerebral and the coronary systems.
This dataset was generated using an iterative active-learning strategy implemented in the ArcaNN software package (https://github.com/arcann-chem/arcann_training) to train machine-learning interatomic potentials for aqueous ZnCl2 solutions. Each active-learning cycle consisted of three stages: training, exploration, and labeling. The initial training set combined configurations generated in this work from enhanced-sampling ab initio molecular dynamics simulations with configurations from a previously reported neural-network-potential study of aqueous ZnCl2. The enhanced-sampling ab initio molecular dynamics simulations involved Zn–Cl separation and the chloride coordination number around Zn²? as collective variables. These configurations served as the seed dataset. Subsequent active-learning cycles expanded the training set by identifying and labeling configurations that were poorly represented by the current models, thereby improving coverage of ion-association states and changes in local coordination and charge-state environments relevant to the solution free-energy landscape. For all selected configurations, single-point calculations of the total energies and atomic forces were performed within density functional theory using the CP2K Quickstep module. Reference calculations employed the revPBE-D3 and r2SCAN exchange-correlation functionals. Motivated by recent work on aqueous Zn²?, the main revPBE calculations omitted D3 dispersion contributions involving Zn²?, while retaining the D3 correction for water and chloride. For comparison, fully dispersion-corrected revPBE-D3 reference calculations were also performed, with D3 applied to all species, including Zn²?. Valence electrons were treated explicitly, while core electrons were represented using norm-conserving Goedecker–Teter–Hutter pseudopotentials. The wave functions were expanded using the mixed Gaussian-and-plane-wave scheme with TZV2P-MOLOPT basis sets for all elements and a 600 Ry auxiliary plane-wave cutoff for the electron density. Self-consistent-field convergence was accelerated using the orbital-transformation and Direct Inversion in the Iterative Subspace algorithms, with a convergence threshold of 10?6. All single-point calculations were performed in periodic orthorhombic cells. The CELL_REF keyword in CP2K was used to define a fixed reference cell with a box length of 25 Å. This treatment ensured a consistent reference for configurations extracted from NpT trajectories with fluctuating cell dimensions. The resulting DFT energies and atomic forces constitute the ground-truth labels used to train the MLIPs. The resulting MLIP was trained for aqueous ZnCl2 solutions spanning concentrations from 0 to 30 molal and a broad pH range, from strongly acidic to strongly basic conditions. Representative examples of configurations included in the MLIP training dataset are provided below. These include 1) Representative configurations from the dataset labeled at the revPBE-D3 level, with D3 dispersion interactions involving Zn2+ excluded (revPBE-wo-D3). 2) Representative configurations from the dataset labeled at the fully dispersion-corrected revPBE-D3 level, with D3 interactions applied to all species, including Zn2+ (revPBE-D3). 3) Representative configurations from the dataset labeled at the r2SCAN level of theory (r2SCAN).
Current methods for atomistic simulations of material systems suffer from limitations which restrict the ability of the simulation to correctly characterize certain material behavior and physical phenomena. Small scale ab initio (AIMD) modeling is highly accurate but is computationally expensive. Classical molecular dynamics (CMD) simulations use interatomic potentials (IPs) to describe larger systems at a reduced computational cost, but with a reduced accuracy. Creating more robust IPs enable more precise CMD simulations. In this thesis, the application of a specific machine learning process,artifical neural networks (ANNs), to the improvement of IPs and MD simulation is discussed.
Traditionally, distribution system planning has focused on steady-state analyses, with limited consideration of dynamic behavior. However, as large or medium-scale inverter-based resources (IBRs), particularly grid-following (GFL) inverters in commercial or industry buildings, become more prevalent, understanding their dynamic impact is essential for grid planning and operation. This article presents an innovative deep-learning (DL)-approach using convolutional neural networks technique to model the GFL inverters. Developed from real grid-tied commercial IBR transient data, these dynamic DL models overcome proprietary constraints by requiring minimal knowledge of internal converter physics while maintaining high accuracy and flexibility. To demonstrate their applicability, the models were incorporated into GridLAB-D, an open-source, three-phase distribution analysis tool. This integration enables dynamic simulations of large-scale distribution networks with high IBR penetration stability analysis. Rigorous testing and validation, aligned with industry standards, confirmed the reliability and efficiency of this approach, paving the way for enhanced planning and operational assessments of modern power systems.
Permeability in reactive porous media evolves in complex ways that are hard to predict. Macroscopic empirical equations are often used to estimate permeability evolution but fail to reflect the impact of pore scale reactions on permeability. This work aims to understand the evolution of permeability in systems where mineral dissolution and precipitation occur simultaneously. Pore network models are used for permeability simulation of a Paluxy sandstone using pore and pore-throat size distributions from the analysis of X-ray CT images. Pore and pore-throat radii are increased and decreased to reflect the effects of dissolution and precipitation reactions. Varying spatial distributions of reactions are simulated and the resulting porosity and permeability values compared with commonly used macroscopic equations. It is observed that when dissolution occurs at the inlet and precipitation at the outlet, porosity increases while permeability decreases. Similar results are also observed in the respective opposite scenario where precipitation occurs at the inlet and dissolution at the outlet. When dissolution and precipitation reactions are randomly distributed throughout the network, porosity increases with little change in permeability that is not captured by the empirical equations. When reactions are controlled by pore and pore-throat sizes, such as dissolution occurring in pores and pore-throats of small size and precipitation in pores and pore-throats of larger size, porosity and permeability decrease. When precipitation occurs in pores and pore-throats of smaller size and dissolution in pores and pore-throats of larger size, porosity and permeability increase and is described relatively well by the Verma-Pruess porosity-permeability equation.
We present a set of multiphase flow simulations where supercritical CO 2 (scCO 2 ) displaces water at hydrostatic conditions within three-dimensional discrete fracture networks that represent paths for potential leakage through caprock above CO 2 storage reservoirs. The simulations are performed to characterize and compare the relative impact of hydraulic and structural heterogeneity in fractured media on the initial movement of scCO 2 through these caprock formations. In one scenario, intrinsic fracture permeabilities are varied stochastically within a fixed network structure. In another scenario, we generate multiple independent, identically distributed network realizations with varying fracture network densities to explore a wide range of geometric and topological configurations. Analysis of the simulations indicates that network structure, specifically connectivity and the presence of hanging fractures, plays a larger role in controlling the displacement of water by scCO 2 than variations in local hydraulic properties. Finally, we identify active surface area of the network as a single-phase feature that could provide a lower bound on the percentage of the network surface area reached by scCO 2 .
Methods and algorithms used for the simulation of elementary power conditioning units buck, boost, and buck-boost, as well as shunt PWM are described. Definitions are given of similar converters and reduced parameters. The various parts of the simulation to be carried out are dealt with; local stability, corrective network, measurements of input-output impedance and global stability. A simulation example is given.
Disordered solids often change their elastic response as they slowly age. Using experiments and simulations, we study how aging disordered planar networks under an applied stress affects their nonlinear elastic response. We are able to modify dramatically the elastic properties of our systems in the nonlinear regime. Using simulations, we study two models for the microscopic evolution of properties of such a material; the first considers changes in the material strength, while the second considers distortions in the microscopic geometry. Both models capture different aspects of the experiments including the encoding of memories of the aging history of the system and the dramatic effects on the material’s nonlinear elastic properties. Our results demonstrate how aging can be used to create complex elastic behavior in the nonlinear regime.
Eddy current flow meters (ECFMs) measure flows of conductive fluids. Recent interest in ECFMs has increased due to applications in advanced nuclear reactors. ECFMs are well suited for such applications, as they can provide non-invasive measurements of flow in fluids that are often difficult to measure. Traditionally, ECFMs are operated using an alternating current at a single frequency, limiting ECFMs to measure average fluid velocities, blockages, or voids. Here, we expand the capabilities of ECFMs by measuring the fluid radial velocity profile of liquid mercury. To accomplish this, we made several ECFM sensitivity measurements at a range of frequencies. Different frequencies vary the electromagnetic skin depth of the device. By adjusting frequencies, we probed the fluid velocity at various radial locations and constructed a flow-velocity profile. The relationship between the ECFM measurements and velocity profile is nonlinear and requires solving an inverse problem. Using electromagnetic finite-element simulations to train a deep neural network (DNN), we created a model that provides a stable general relationship between the sensitivity measurements of an ECFM and the fluid velocity profile. Using ECFM measurements of liquid mercury, our DNN model calculates a flow profile that agrees well with computational fluid dynamics (CFD) simulations. This technique has potential to improve flow monitoring for optimization, safe operation of conductive fluid loops, and/or validating complex CFD models.
Liquid argon time projection chamber (LArTPC) detector technology offers a wealth of high-resolution information on particle interactions, and leveraging that information to its full potential requires sophisticated automated reconstruction techniques. Here, this article describes NUGRAPH 2, a graph neural network for low-level reconstruction of simulated neutrino interactions in a LArTPC detector. Simulated neutrino interactions in the MicroBooNE detector geometry are described as heterogeneous graphs, with energy depositions on each detector plane forming nodes on planar subgraphs. The network utilizes a multihead attention message-passing mechanism to perform background filtering and semantic labeling on these graph nodes, identifying those associated with the primary physics interaction with 98.0% efficiency and labeling them according to particle type with 94.9% efficiency. The network operates directly on detector observables across multiple two-dimensional representations but utilizes a three-dimensional-context-aware mechanism to encourage consistency between these representations. Model inference takes 0.12 s / event on a CPU and 0.005 s / event batched on a GPU. This architecture is designed to be a general-purpose solution for particle reconstruction in neutrino physics, with the potential for deployment across a broad range of detector technologies, and offers a core convolution engine that can be leveraged for a variety of tasks beyond the two described in this paper.
We consider r -process nucleosynthesis in outflows from black hole accretion discs formed in double neutron star and neutron star–black hole mergers. These outflows, powered by angular momentum transport processes and nuclear recombination, represent an important – and in some cases dominant – contribution to the total mass ejected by the merger. Here we calculate the nucleosynthesis yields from disc outflows using thermodynamic trajectories from hydrodynamic simulations, coupled to a nuclear reaction network. We find that outflows produce a robust abundance pattern around the second r -process peak (mass number A ~ 130), independent of model parameters, with significant production of A < 130 nuclei. This implies that dynamical ejecta with high electron fraction may not be required to explain the observed abundances of r -process elements in metal poor stars. Disc outflows reach the third peak (A ~ 195) in most of our simulations, although the amounts produced depend sensitively on the disc viscosity, initial mass or entropy of the torus, and nuclear physics inputs. Some of our models produce an abundance spike at A = 132 that is absent in the Solar system r -process distribution. The spike arises from convection in the disc and depends on the treatment of nuclear heating in the simulations. We conclude that disc outflows provide an important – and perhaps dominant – contribution to the r -process yields of compact binary mergers, and hence must be included when assessing the contribution of these systems to the inventory of r -process elements in the Galaxy.
Tetrahedral liquids exhibit intriguing thermodynamic and transport properties because of the various ways tetrahedra can be packed and connected. Recently, an unusual temperature dependence of the stretching exponent β in a model tetrahedral liquid ZnCl 2 from T m + 85 K to T m + 35 K has been reported using neutron-spin echo spectroscopy. This discovery stands in sharp contrast to other glass-forming liquids. In this study, we conducted neural network force field driven molecular dynamic simulations of ZnCl 2 . We found a non-monotonic temperature dependence of β from liquid to supercooled liquid temperatures. Further structural decomposition and dynamic analysis suggest that this unusual dynamic behavior is a result of the competition between the decrease in the diversity of tetrahedra motifs (structural heterogeneity) and the increase in glassy dynamic heterogeneity. Furthermore, this result may contribute to new understandings of the structural relaxation of other network liquids.