Automatic model generation for signal transduction with applications to MAP-Kinase pathways
We describe a general approach to automatic model generation in the description of dynamic regulatory networks.
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We describe a general approach to automatic model generation in the description of dynamic regulatory networks.
Strictly evolutionary approaches to improving the air transport system a highly complex network of interacting systems no longer suffice in the face of demand that is projected to double or triple in the near future. Thus evolutionary approaches should be augmented with active design methods. The ability to actively design, optimize and control a system presupposes the existence of predictive modeling and reasonably well-defined functional dependences between the controllable variables of the system and objective and constraint functions for optimization. Following recent advances in the studies of the effects of network topology structure on dynamics, we investigate the performance of dynamic processes on transport networks as a function of the first nontrivial eigenvalue of the network's Laplacian, which, in turn, is a function of the network s connectivity and modularity. The last two characteristics can be controlled and tuned via optimization. We consider design optimization problem formulations. We have developed a flexible simulation of network topology coupled with flows on the network for use as a platform for computational experiments.
The number of spaceflight bioscience mission opportunities is too small to allow all relevant biological and environmental parameters to be experimentally identified. Simulated spaceflight experiments in ground-based facilities (GBFs), such as clinostats, are each suitable only for particular investigations -- a rotating-wall vessel may be 'simulated microgravity' for cell differentiation (hours), but not DNA repair (seconds) -- and introduce confounding stimuli, such as motor vibration and fluid shear effects. This uncertainty over which biological mechanisms respond to a given form of simulated space radiation or gravity, as well as its side effects, limits our ability to baseline spaceflight data and validate mission science. Machine learning techniques autonomously identify relevant and interdependent factors in a data set given the set of desired metrics to be evaluated: to automatically identify related studies, compare data from related studies, or determine linkages between types of data in the same study. System-of-systems (SoS) machine learning models have the ability to deal with both sparse and heterogeneous data, such as that provided by the small and diverse number of space biosciences flight missions; however, they require appropriate user-defined metrics for any given data set. Although machine learning in bioinformatics is rapidly expanding, the need to combine spaceflight/GBF mission parameters with omics data is unique. This work characterizes the basic requirements for implementing the SoS approach through the System Map (SM) technique, a composite of a dynamic Bayesian network and Gaussian mixture model, in real-world repositories such as the GeneLab Data System and Life Sciences Data Archive. The three primary steps are metadata management for experimental description using open-source ontologies, defining similarity and consistency metrics, and generating testing and validation data sets. Such approaches to spaceflight and GBF omics data may soon enable unique insight into which measured phenomena correlate to biological mechanisms that are truly affected by spaceflight conditions; which are most likely to be confounded by other variables; and which are insufficiently characterized, significantly increasing existing and future science return from ISS and spaceflight missions.
The Lunar Laser Ranging (LLR) experiment has accumulated 50 years of range data of improving accuracy from ground stations to the laser retroreflector arrays (LRAs) on the lunar surface. The upcoming decade offers several opportunities to break new ground in data precision through the deployment of the next generation of single corner-cube lunar retroreflectors and active laser transponders. This is likely to expand the LLR station network. Lunar dynamical models and analysis tools have the potential to improve and fully exploit the long temporal baseline and precision allowed by millimetric LLR data. Some of the model limitations are outlined for future efforts. Differential observation techniques will help mitigate some of the primary limiting factors and reach unprecedented accuracy. Such observations and techniques may enable the detection of several subtle signatures required to understand the dynamics of the Earth- Moon system and the deep lunar interior. LLR model improvements would impact multi- disciplinary fields that include lunar and planetary science, Earth science, fundamental physics, celestial mechanics and ephemerides.
NASA Glenn Research Center is focused on supporting NASA goals in several mission areas from Space Exploration and Aeronautics to Science. NASA GRC is exploring how quantum metrology, models, and free-space testbeds can be integrated with NASA’s aerospace competency needs to provide an understanding of how spaceflight components work together in Quantum Information Systems. In this presentation an overview of potential focus areas for quantum systems along with current efforts to enable research and analysis of quantum systems for NASA applications will be discussed. As such, we provide an overview of device measurement capability within NASA’s Quantum Metrology Laboratory (NQML), dynamic quantum network modeling via the NASA Quantum Communications Analysis Suite (NQCAS) simulation tool, and plans for instituting an aero quantum testbed platform.
This study developed a market-based coordination framework that allows for exchanging information on gas off-takes as well as constraints between a power sector model. This includes unit commitment, economic dispatch, and a dynamic gas network simulation model. The framework was then tested using real power- and gas-system data from Colorado.
Energy storage systems and flexible loads have attracted significant interests due to their capabilities to provide various grid services. In this paper, the flexibilities are optimally allocated among multiple distributed energy resource aggregators with energy storage systems and flexible buildings by the utility coordinator through market-based co-optimization. An iterative market clearing algorithm is developed to determine the optimal energy and ancillary service prices, with consideration of both local dynamics and network constraints. Simulation results demonstrate the effectiveness of the proposed algorithm and the benefits of co-optimizing the energy and ancillary service markets.
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Residential air conditioners and heat pumps often experience faults due to inadequate maintenance, which can severely reduce efficiency or even cause system failure. Common issues include dirty or clogged air filters and refrigerant leaks. These problems degrade performance and increase energy use and operating costs. This study presents a smart thermostat with embedded artificial intelligence to detect such faults and alert homeowners when maintenance is needed. The thermostat uses low-cost measurements—including return-air temperature, relative humidity, supply-air temperature, outdoor-air temperature, and condenser subcooling—to identify abnormal operations. Because different faults produce distinct response patterns, tailored algorithms are developed to recognize characteristic fault signatures. The investigation is built on a detailed co-simulation platform that couples EnergyPlus with the DOE/ORNL Heat Pump Design Model (HPDM). EnergyPlus represents the building’s dynamic environment, while HPDM is a high-fidelity, hardware-based model that can simulate fault-free performance as well as a wide range of faults, including gradual degradation such as minor refrigerant leakage. This platform provides a virtual training and testing environment that helps distinguish fault-induced behavior from normal operation and supports development of robust diagnostic algorithms. Using this framework, a Dynamic Bayesian Network was developed to identify two common faults—gradual refrigerant charge loss and indoor airflow blockage—and the AI-embedded thermostat was verified through annual building simulations.
Resilient intermodal freight networks are vital for sustaining supply chains amid increasing threats from natural hazards and cyberattacks. Transportation resilience has been widely studied; understanding how random and targeted disruptions affect structural connectivity and functional performance remains a key challenge. To address this, this study evaluates the robustness of the US intermodal freight network, which consists of rail and water modes, using a simulation-based framework that integrates graph-theoretic metrics with flow-weighted centrality measures. Disruption scenarios are examined, including random failures as well as targeted node and edge removals based on static and dynamically updated degree and betweenness centrality. To reflect more realistic conditions, flow-weighted degree centralities (WDC) and partial node degradation are considered. Two resilience indicators are used: (1) the size of the giant connected component to measure structural connectivity; and (2) flow-weighted network efficiency (NE) to assess freight mobility under disruption. The results show that progressively degrading nodes ranked by WDC to 60% of their original functionality causes a sharper decline in normalized NE, for up to approximately 45 affected nodes, than complete failure (100% loss of functionality) applied to nodes targeted by weighted betweenness centrality or selected at random. This highlights how partial degradation of high-tonnage hubs can produce disproportionately large functional losses. The findings emphasize the need for resilience strategies that go beyond network topology to incorporate freight flow dynamics.
Computational self-sufficiency - the making of communication decisions on the basis of locally available information that is already in place, rather than on the basis of information residing at other entities - is a fundamental principle of Delay-Tolerant Networking. Contact Graph Routing is an attempt to apply this principle to the problem of dynamic routing in an interplanetary DTN. Testing continues, but preliminary results are promising.
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Recently, machine learning models have shown many successes in various applications in science and technology. In this work, we focus on the charged particle dynamics, with the development of a class of symplectic neural networks, including a linear version, SympMat, and a nonlinear version, HénonNet. Both are designed to preserve the structure of Hamiltonian systems. We show that they can be used to model relevant Hamiltonian systems of interest in plasma physics and astrophysics, for linear and nonlinear charged particle dynamics, with the potential to bridge multi-scale simulations. These symplectic neural networks are adapted to the applications in plasma simulations and particle-wave interaction with parametric dependence and periodicity, where we have investigated their performance and accuracy. In particular, SympMat is shown to outperform the traditional Boris particle pusher down to the sub-gyroperiod scale in the case of charged particles in uniform magnetic fields. HénonNet successfully predicts the hot electron distribution, which is validated against theoretical results. These results highlight the potential of symplectic neural networks as a trajectory integrator for particle-in-cell simulations or a fast surrogate to replace conventional numerical schemes.
Deep Space Network for two-way communications with unmanned spacecraft at planetary distances - Vol. 2
Increasing occurrences of natural disasters and grid emergency events consistently challenge the safe and reliable operations of power systems. During such emergency situations, system operators may proactively shed load to mitigate risks. However, uncoordinated implementation of load shedding may disrupt electricity supply and even lead to cascading failures. Meanwhile, it is crucial to address potential biases affecting different customers when executing load shedding. This paper addresses the dynamic topology reconfiguration problem for networked microgrids with distributed energy resources under emergency conditions. Specifically, we propose a novel rolling-horizon optimization model that integrates fairness-aware constraints into the networked microgrid topology reconfiguration. Unlike existing approaches that focus solely on efficiency or apply fairness considerations in static settings, our method explicitly incorporates temporal fairness constraints to restrict repeated or excessive load curtailment for load blocks. Moreover, the fairness-aware constraints are specifically developed for the context of dynamic networked microgrid topology reconfiguration, and are designed to be convex or amenable to linear reformulations, which offers a more tractable alternative to traditional models with non-convex formulations. Numerical studies on a modified IEEE 13-bus system and a larger-sized SMART-DS networked microgrid system demonstrate the performance of the proposed algorithm towards more fairness-aware networked microgrid topology reconfiguration decision-making.
In this work, we develop a machine learning (ML) model with aleatoric uncertainty for the low energy beam transport (LEBT) region of the LANSCE linear accelerator in which we model the transport of a space-charge-dominated 750 keV proton beam through a lattice of 22 quadrupole magnets. Our ML model is developed based on data generated by a Kapchinsky–Vladimirsky (KV) envelope model of beam transport. We show that a recurrent neural network can be used as a dynamical surrogate model for fast prediction of the LEBT beam envelope. Furthermore, we endow the model with the prediction of aleatoric uncertainty and compare three different approaches. We demonstrate that the ML-based uncertainty quantification models are well calibrated and produce good estimates of the regions where the model is less certain about its predictions. This ML framework is a necessary step in the development of a real-time virtual diagnostic tool with uncertainty quantification that can be integrated into more complex downstream tasks (e.g., adaptive control or learning flexible control policies via reinforcement learning) for improved efficiency in beam operations. In future work, we plan to expand on this preliminary study by considering more realistic envelope models that include longitudinal momentum spread and dispersive effects in bending magnets, as well as particle tracking codes with 3D space charge (such as and ). Published by the American Physical Society 2024
This paper explores the applications of Fusion Graph Neural Network (FuGNN) on power distribution systems. FuGNN effectively models dynamic networks with evolving topology and features. Applied to power system network reconfiguration, FuGNN demonstrates its feasibility in optimizing switch configurations to minimize unserved loads and operational costs during extreme events. Additionally, FuGNN supports various downstream tasks, such as node feature prediction, further enhancing its versatility and applicability in power system resilience.
Reactive molecular dynamics simulations enable detailed understanding of solvent effects on chemical reaction mechanisms and reaction rates. While classical molecular dynamics using reactive force fields allows significantly longer simulation time scales and larger system sizes compared with ab initio molecular dynamics, constructing reactive force fields is a difficult and complex task. In this work, we describe a general approach following the Empirical Valence Bond (EVB) framework for constructing ab initio reactive force fields for condensed phase simulations by combining physics-based methods with neural networks (PB/NN). The physics-based terms ensure correct asymptotic behavior of electrostatic, polarization, and dispersion interactions, and are compatible with existing solvent force fields. Neural networks are utilized for versatile description of short-range orbital interactions within the transition state region, and accurate rendering of vibrational motion of the reacting complex. Herein, we demonstrate our methodology for a simple deprotonation reaction of the 1-ethyl-3-methylimidazolium (EMIM+) cation with acetate to form 1-ethyl- 3-methylimidazol-2-ylidene and acetic acid. Our PB/NN force field exhibits ~ 1 kJ/mol MAE accuracy within the transition state region for the gas-phase complex. To characterize solvent modulation of the reaction profile, we compute potentials of mean force (PMFs) for the gas-phase reaction as well as the reaction within a four ion cluster, and benchmark against ab initio molecular dynamics simulations. We find that the surrounding ionic environment significantly destabilizes formation of the carbene product, and we show that this effect is accurately captured by the reactive force field. By construction, the PB/NN potential may be directly employed for simulations of other solvents/chemical environments without additional parameterization.