Gene regulation networks with signaling and cell division in development simulations
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gene regulation↗
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Compressing Hamiltonians with ab initio downfolding for simulating strongly-correlated materials on quantum computers
The accurate first-principles description of strongly correlated materials is an important and challenging problem in condensed matter physics. Ab initio downfolding has emerged as a way of deriving compressed many-body Hamiltonians that maintain the essential physics of strongly correlated materials. The solution of these material-specific models is still exponentially difficult to generate on classical computers, but quantum algorithms allow for a significant speed-up in obtaining the ground states of these compressed Hamiltonians. Here, we demonstrate that using quantum algorithms to obtain the properties of downfolded Hamiltonians can indeed yield high-fidelity solutions. By combining ab initio downfolding and variational quantum eigensolvers, we correctly predict the antiferromagnetic state of one-dimensional cuprate Ca 2 Cu O 3 , the excitonic ground state of monolayer W Te 2 , and the charge-ordered state of correlated metal Sr VO 3 . Numerical simulations using a classical tensor network implementation of variational quantum eigensolvers allow us to simulate large models with up to 54 qubits and encompassing up to four bands in the correlated subspace, which is indicative of the complexity that our framework can address. Through these methods we demonstrate the potential of classical preoptimization and downfolding techniques for enabling efficient materials simulation using quantum algorithms.
Alvertis, Antonios M. [NASA, Ames; LBNL, Berkeley]↗
A Participation Factor-Based Approach for Defining the EMT Model Boundary for Power System Simulations with Inverter-Based Resources
The increasing penetration of inverter-based resources (IBRs) introduces new challenges to power system simulations, particularly with the emergence of fast electromagnetic transient (EMT) dynamics and sub-synchronous oscillations (SSO) that require time-consuming EMT simulations. To reduce the time cost for simulating a large-scale power grid with IBRs, this paper proposes a novel participation factor-based approach for defining a critical zone for detailed EMT modeling and simulations, which includes the IBRs, synchronous generators, and the network components participating significantly in simulated contingencies. Both model-based and response-based methods are introduced for the estimation of participation factors (PFs). The case study on the 240-bus Western Electricity Coordinating Council (WECC) system demonstrates that the EMT zone determined by the proposed approach can effectively capture power system dynamics involving IBRs.
EMT simulation↗
Telemetry Simulation Assembly Implementation in the DSN
The telemetry simulation was implemented as part of the MARK IV network implementation project. The telemetry simulation assembly (TSA) is replacing the Simulation Conversion Assembly (SCA) throughout the DSN. The development of the TSA is discussed, and the design is described to the block diagram level.
Alberda, M. E.↗
Computational Power of Random Quantum Circuits in Arbitrary Geometries
Empirical evidence for a gap between the computational powers of classical and quantum computers has been provided by experiments that sample the output distributions of two-dimensional quantum circuits. Many attempts to close this gap have utilized classical simulations based on tensor network techniques, and their limitations shed light on the improvements to quantum hardware required to frustrate classical simulability. In particular, quantum computers having in excess of approximately 50 qubits are primarily vulnerable to classical simulation due to restrictions on their gate fidelity and their connectivity, the latter determining how many gates are required (and, therefore, how much infidelity is suffered) in generating highly entangled states. Here, we describe recent hardware upgrades to Quantinuum’s H2 quantum computer, enabling it to operate on up to 56 qubits with arbitrary connectivity and 99.843(5)% two-qubit gate fidelity. We define a class of circuits with random geometries that become hard to classically simulate in very low depth and implement them utilizing the flexible connectivity of H2. A careful analysis demonstrating the fast saturation of classical simulation complexity with depth indicates that H2 can yield data well beyond the reach of state-of-the art classical simulation methods at unprecedented fidelities. We find that the considerable difficulty of classically simulating H2 is likely limited only by qubit number, demonstrating the promise and scalability of the quantum charge-coupled device architecture as continued progress is made toward building larger machines. Published by the American Physical Society 2025
DeCross, M.↗
Calibrating Bayesian generative machine learning for Bayesiamplification
Recently, combinations of generative and Bayesian deep learning have been introduced in particle physics for both fast detector simulation and inference tasks. These neural networks aim to quantify the uncertainty on the generated distribution originating from limited training statistics. The interpretation of a distribution-wide uncertainty however remains ill-defined. We show a clear scheme for quantifying the calibration of Bayesian generative machine learning models. For a Continuous Normalizing Flow applied to a low-dimensional toy example, we evaluate the calibration of Bayesian uncertainties from either a mean-field Gaussian weight posterior, or Monte Carlo sampling network weights, to gauge their behaviour on unsteady distribution edges. Well calibrated uncertainties can then be used to roughly estimate the number of uncorrelated truth samples that are equivalent to the generated sample and clearly indicate data amplification for smooth features of the distribution.
97 MATHEMATICS AND COMPUTING↗
A carrier sensed multiple access protocol for high data base rate ring networks
The results of the study of a simple but effective media access protocol for high data rate networks are presented. The protocol is based on the fact that at high data rates networks can contain multiple messages simultaneously over their span, and that in a ring, nodes used to detect the presence of a message arriving from the immediate upstream neighbor. When an incoming signal is detected, the node must either abort or truncate a message it is presently sending. Thus, the protocol with local carrier sensing and multiple access is designated CSMA/RN. The performance of CSMA/RN with TTattempt and truncate is studied using analytic and simulation models. Three performance factors, wait or access time, service time and response or end-to-end travel time are presented. The service time is basically a function of the network rate, it changes by a factor of 1 between no load and full load. Wait time, which is zero for no load, remains small for load factors up to 70 percent of full load. Response time, which adds travel time while on the network to wait and service time, is mainly a function of network length, especially for longer distance networks. Simulation results are shown for CSMA/RN where messages are removed at the destination. A wide range of local and metropolitan area network parameters including variations in message size, network length, and node count are studied. Finally, a scaling factor based upon the ratio of message to network length demonstrates that the results, and hence, the CSMA/RN protocol, are applicable to wide area networks.
Foudriat, E. C.↗
Extremely high data-rate, reliable network systems research
Significant progress was made over the year in the four focus areas of this research group: gigabit protocols, extensions of metropolitan protocols, parallel protocols, and distributed simulations. Two activities, a network management tool and the Carrier Sensed Multiple Access Collision Detection (CSMA/CD) protocol, have developed to the point that a patent is being applied for in the next year; a tool set for distributed simulation using the language SIMSCRIPT also has commercial potential and is to be further refined. The year's results for each of these areas are summarized and next year's activities are described.
Foudriat, E. C.↗
Evolution at the Edge: Real-Time Evolution for Neuromorphic Engine Control
Neuromorphic computing systems are attractive for real-time control at the edge because of their low power operation, real-time processing capabilities and their potential ability to do online learning. In this work, we describe an approach for performing real-time evolution of spiking neural networks for neuromorphic systems at the edge called Neuromorphic Optimization using Dynamic Evolutionary Systems or NODES. We apply this approach to real-time combustion engine control and develop an engine-specific hardware platform for NODES called FireBox. We demonstrate how the real-time evolution approach works in simulation and the performance of networks trained in simulation on the physical engine.
Maldonado Puente, Bryan [ORNL] (ORCID:000000033880↗
Neural-Network-Enhanced COTSIM: Advancing Predictive Capabilities for Fast DIII-D Simulations
Sustaining fusion reactions in tokamaks requires heating plasma to thermonuclear temperatures while maintaining confinement and stability. Neutral beam injection (NBI) provides heating, current drive, torque, and fueling, while electron cyclotron (EC) waves are widely used for heating and current drive; together, these actuators shape the plasma current, temperature, and density profiles. The control-oriented tokamak simulator (COTSIM), a predictive, control-oriented code, has been enhanced with neural-network surrogates for transport and sources. Turbulent transport is predicted by MMMnet—a neural-network version of the updated multimode model (MMM 9.0.10)—with significantly reduced computation time relative to MMM; neoclassical transport follows the Chang–Hinton model. NUBEAMnet, a surrogate of the Monte Carlo NUBEAM module, predicts beam-driven heating, current, and torque. EC heating and current drive use a control-oriented, empirically scaled source model; plasma resistivity follows the Spitzer formulation; bootstrap current uses the Sauter model. Equilibrium is computed using both prescribed and fixed-boundary solvers (FBSs), and the pedestal structure is modeled with an empirical pedestal model. For a representative DIII-D discharge, COTSIM predicts electron and ion temperature and safety-factor profiles in close agreement with TRANSP predictive and interpretive simulations while extending predictions through the pedestal region to the plasma edge (versus 80% of the minor radius in TRANSP). Furthermore, the equivalent COTSIM simulation runs in under 3 min compared to about 2 h for TRANSP, enabling rapid scenario planning, optimization of tokamak operation, and between-pulse control design.
Control-oriented tokamak simulator (COTSIM)↗
Recent Weakening of the Global Radiative Feedback
Earth's climate stability, characterized by the global radiative feedback parameter (𝜆), varies decadally due to changing surface temperature patterns. Recent variations in 𝜆 are poorly understood as coordinated model simulations typically end in 2014. We apply a convolutional neural network trained on climate model simulations to observation-based surface temperature reconstructions to estimate variations in 𝜆 up to 2025. We find that 𝜆 reached a minimum (maximum stability) around the mid 1990s (𝜆 ≃ −3 Wm −2 /K), but has since weakened significantly (𝜆 ≃ −2 Wm −2 /K). We confirm these results with climate model simulations extended to 2022. The recent 𝜆 weakening is not significantly affected by El Niño Southern Oscillation or Pacific Decadal Oscillation. Attribution reveals that warming in the subtropical Northeast Pacific is an important driver of the recently weakened feedback, confirmed by targeted experiments in E3SMv2. Our approach enables near real-time monitoring of Earth's climate stability.
54 ENVIRONMENTAL SCIENCES↗
MicroRNA Expression Profiles in Cultured Human Fibroblasts in Space
Microgravity, or an altered gravity environment from the static 1g, has been shown to influence global gene expression patterns and protein levels in living organisms. However, it is unclear how these changes in gene and protein expressions are related to each other or are related to other factors regulating such changes. A different class of RNA, the small non-coding microRNA (miRNA), can have a broad effect on gene expression networks by mainly inhibiting the translation process. Previously, we investigated changes in the expression of miRNA and related genes under simulated microgravity conditions on the ground using the NASA invented bioreactor. In comparison to static 1 g, simulated microgravity altered a number of miRNAs in human lymphoblastoid cells. Pathway analysis with the altered miRNAs and RNA expressions revealed differential involvement of cell communication and catalytic activity, as well as immune response signaling and NGF activation of NF-kB pathways under simulated microgravity condition. The network analysis also identified several projected networks with c- Rel, ETS1 and Ubiquitin C as key factors. In a flight experiment on the International Space Station (ISS), we will investigate the effects of actual spaceflight on miRNA expressions in nondividing human fibroblast cells in mostly G1 phase of the cell cycle. A fibroblast is a type of cell that synthesizes the extracellular matrix and collagen, the structural framework for tissues, and plays a critical role in wound healing and other functions. In addition to miRNA expressions, we will investigate the effects of spaceflight on the cellular response to DNA damages from bleomycin treatment.
Wu, Honglu↗
Flight and Direct to Earth/Space Relay Communication System Architecture for GSFC CubeSat Missions
The CubeSat platform is finding increasing use in space science applications due to its low cost and comparative ease of launch. It is becoming a key scientific discovery tool in low Earth orbit (LEO) and beyond, including geosynchronous equatorial orbit (GEO), the Lagrange Points, Lunar missions, and more. The increasing complexity of these missions and their scientific goals must be supported by equal advancements in communications technology. Higher data rates and greater reliability are required every year. However, the reduced Size, Weight, and Power (SWaP) constraints of CubeSat platforms introduce unique challenges in the area of satellite communications. There is currently a lack of communication equipment tailored specifically to the CubeSat platform. This lack of standardized, tested equipment extends development time and reduces mission confidence. Furthermore, missions utilizing the CubeSat platform are often subject to more difficult design constraints. Antenna placement, size, and pointing are often subordinate to the requirements of the payload instruments and mission goals. Traditional link margin estimation techniques are insufficient in these cases, as they emphasize worst case scenarios. In reality the actual link parameters may vary widely even during a single pass. This presents new challenges in predicting communications performance and scheduling ground station contacts, but also new opportunities for improving efficiency. This paper presents the integration, testing, and validation process for a new software defined radio (SDR) designed for the CubeSat platform in conjunction with Vulcan Wireless, Inc. The SDR is planned for use on 5 upcoming CubeSat missions at NASAs Goddard Space Flight Center (GSFC) including a Geosynchronous Transfer Orbit (GTO) mission and it may also serve as a standard and well-tested option for future missions by enabling a standardized, rapid and low cost CubeSat communication system network integration process. Detailed simulations have been developed to estimate the communication performance of these missions, taking the unique antenna placements and attitude behavior of each satellite into account. These simulations allow a much more accurate analysis of the expected link margin, which varies considerably during each pass for the NASA Space Relay (SR) and Direct to Earth (DTE) network. The modelling procedures are outlined, and the results are used to predict communications performance of the missions.
Space Networks↗
The Deep Impact Network Experiment Operations Center Monitor and Control System
The Interplanetary Overlay Network (ION) software at JPL is an implementation of Delay/Disruption Tolerant Networking (DTN) which has been proposed as an interplanetary protocol to support space communication. The JPL Deep Impact Network (DINET) is a technology development experiment intended to increase the technical readiness of the JPL implemented ION suite. The DINET Experiment Operations Center (EOC) developed by JPL's Protocol Technology Lab (PTL) was critical in accomplishing the experiment. EOC, containing all end nodes of simulated spaces and one administrative node, exercised publish and subscribe functions for payload data among all end nodes to verify the effectiveness of data exchange over ION protocol stacks. A Monitor and Control System was created and installed on the administrative node as a multi-tiered internet-based Web application to support the Deep Impact Network Experiment by allowing monitoring and analysis of the data delivery and statistics from ION. This Monitor and Control System includes the capability of receiving protocol status messages, classifying and storing status messages into a database from the ION simulation network, and providing web interfaces for viewing the live results in addition to interactive database queries.
Delay/Disruption Tolerant Network (DTN)↗
Axisymmetric Two-Dimensional Modeling of No Vent Filling of a Cryogenic Tank using Generalized Fluid System Simulation Program
This paper presents preliminary analysis using a finite volume based computational method for network flow analysis for the simulation of chill and fill of a cryogenic tank. An axisymmetric two-dimensional model of a spherical tank was developed using a nodal approach. No Vent Filling (NVF) was accomplished using a Thermodynamic Vent System assisted injector where the injector was cooled by the cold gas generated by Joule-Thompson expansion of the liquid propellant. The numerical model accounts for a) different regimes of pool boiling heat transfer, b) condensation of vapor around spray droplets, and c) condensation of vapor at the interface of the cooled injector and ullage. The numerical predictions of tank pressure, filling rate, and wall temperatures were compared with the test data and one-dimensional (1D) model predictions. It was demonstrated that the axisymmetric 2D model provided a more realistic prediction than the 1D model.
Cryogenics↗
Assessing the Feasibility of Bordered Block Diagonal Reordering in Power System Matrices using Fully Convolutional Network
In electromagnetic transient (EMT) simulations for power systems and inverter-based resources (IBRs), the arrangement of states within the system's linear equations, represented by matrix A in Ax=b, is critical. The state ordering in matrix A can highlight distinct characteristics of the system's graph, and identifying an optimal state ordering is crucial for efficient computation. The choice of state ordering, however, is dependent on the solver used, as each solver may perform optimally with different matrix patterns. With a wide array of matrix reordering algorithms available, selecting the most suitable one becomes challenging without insights into the matrix's ideal configuration. To address this, the paper proposes a fully convolutional network (FCN) to evaluate the reordering potential of the A matrix into a bordered block diagonal (BBD) pattern, which is commonly observed in power system and IBR modeling. The FCN's assessment aims to streamline the solver's operation, which in turn could substantially reduce the computational time required to find a solution.
Xia, Qianxue↗
Wavelet and Multiresolution Analysis for Finite Element Networking Paradigms
This paper presents a final report on Wavelet and Multiresolution Analysis for Finite Element Networking Paradigms. The focus of this research is to derive and implement: 1) Wavelet based methodologies for the compression, transmission, decoding, and visualization of three dimensional finite element geometry and simulation data in a network environment; 2) methodologies for interactive algorithm monitoring and tracking in computational mechanics; and 3) Methodologies for interactive algorithm steering for the acceleration of large scale finite element simulations. Also included in this report are appendices describing the derivation of wavelet based Particle Image Velocity algorithms and reduced order input-output models for nonlinear systems by utilizing wavelet approximations.
Kurdila, Andrew J.↗
Uncontrolled Learning: Codesign of Neuromorphic Hardware Topology for Neuromorphic Algorithms
Neuromorphic computing has the potential to revolutionize future technologies and our understanding of intelligence, yet it remains challenging to realize in practice. The learning-from-mistakes algorithm, inspired by the brain's simple learning rules of inhibition and pruning, is one of the few brain-like training methods. This algorithm is implemented in neuromorphic memristive hardware through a codesign process that evaluates essential hardware trade-offs. While the algorithm effectively trains small networks as binary classifiers and perceptrons, performance declines significantly with increasing network size unless the hardware is tailored to the algorithm. This work investigates the trade-offs between depth, controllability, and capacity—the number of learnable patterns—in neuromorphic hardware. This highlights the importance of topology and governing equations, providing theoretical tools to evaluate a device's computational capacity based on its measurements and circuit structure. The findings show that breaking neural network symmetry enhances both controllability and capacity. Additionally, by pruning the circuit, neuromorphic algorithms in all-memristive circuits can utilize stochastic resources to create local contrasts in network weights. Through combined experimental and simulation efforts, the parameters are identified that enable networks to exhibit emergent intelligence from simple rules, advancing the potential of neuromorphic computing.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗