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At least 433 records · Page 24

Dynamic X-ray diffraction sampling for protein crystal positioning

A sparse supervised learning approach for dynamic sampling (SLADS) is described for dose reduction in diffraction-based protein crystal positioning. Crystal centering is typically a prerequisite for macromolecular diffraction at synchrotron facilities, with X-ray diffraction mapping growing in popularity as a mechanism for localization. In X-ray raster scanning, diffraction is used to identify the crystal positions based on the detection of Bragg-like peaks in the scattering patterns; however, this additional X-ray exposure may result in detectable damage to the crystal prior to data collection. Dynamic sampling, in which preceding measurements inform the next most information-rich location to probe for image reconstruction, significantly reduced the X-ray dose experienced by protein crystals during positioning by diffraction raster scanning. The SLADS algorithm implemented herein is designed for single-pixel measurements and can select a new location to measure. In each step of SLADS, the algorithm selects the pixel, which, when measured, maximizes the expected reduction in distortion given previous measurements. Ground-truth diffraction data were obtained for a 5 µm-diameter beam and SLADS reconstructed the image sampling 31% of the total volume and only 9% of the interior of the crystal greatly reducing the X-ray dosage on the crystal. Furthermore, by using in situ two-photon-excited fluorescence microscopy measurements as a surrogate for diffraction imaging with a 1 µm-diameter beam, the SLADS algorithm enabled image reconstruction from a 7% sampling of the total volume and 12% sampling of the interior of the crystal. When implemented into the beamline at Argonne National Laboratory, without ground-truth images, an acceptable reconstruction was obtained with 3% of the image sampled and approximately 5% of the crystal. The incorporation of SLADS into X-ray diffraction acquisitions has the potential to significantly minimize the impact of X-ray exposure on the crystal by limiting the dose and area exposed for image reconstruction and crystal positioning using data collection hardware present in most macromolecular crystallography end-stations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Joint Spectrum Access and Power Control in Air-Air Communications - A Deep Reinforcement Learning Based Approach

This paper considers the dynamic spectrum access and power control problem in a single-hop point-to-point Air-Air Communication Network (AACN). Due to spectrum scarcity, we assume the number of Aircraft-to-Aircraft (A2A) communication links is greater than that of the available channels, such that some communication links need to share the same channel, causing co-channel interference. We formulate the joint channel selection and power control optimization problem to maximize the Weighted Sum Spectral Efficiency (WSSE). A distributed and dynamic deep Q learning-based algorithm is proposed to find the optimal solution. Specifically, we design two different policies that are trained by conducting a trial-and-error scheme. Each communication link can achieve the optimal policy by exploiting the local information from its neighbors, and this distributive approach make it scalable to large networks. Finally, our experimental results demonstrate the effectiveness of the proposed solution in various AACN scenarios.

Zhe Wang↗

Joint Spectrum Access and Power Control in Air-Air Communications - A Deep Reinforcement Learning Based Approach

This paper considers the dynamic spectrum access and power control problem in a single-hop point-to-point Air-Air Communication Network (AACN). Due to spectrum scarcity, we assume the number of Aircraft-to-Aircraft (A2A) communication links is greater than that of the available channels, such that some communication links need to share the same channel, causing co-channel interference. We formulate the joint channel selection and power control optimization problem to maximize the Weighted Sum Spectral Efficiency (WSSE). A distributed and dynamic deep Q learning-based algorithm is proposed to find the optimal solution. Specifically, we design two different policies that are trained by conducting a trial-and-error scheme. Each communication link can achieve the optimal policy by exploiting the local information from its neighbors, and this distributive approach make it scalable to large networks. Finally, our experimental results demonstrate the effectiveness of the proposed solution in various AACN scenarios.

Zhe Wang↗

Automated characterization of spatial and dynamical heterogeneity in supercooled liquids via implementation of machine learning

Abstract A computational approach by an implementation of the principle component analysis (PCA) with K -means and Gaussian mixture (GM) clustering methods from machine learning algorithms to identify structural and dynamical heterogeneities of supercooled liquids is developed. In this method, a collection of the average weighted coordination numbers ( W C N s ‾ ) of particles calculated from particles’ positions are used as an order parameter to build a low-dimensional representation of feature (structural) space for K -means clustering to sort the particles in the system into few meso-states using PCA. Nano-domains or aggregated clusters are also formed in configurational (real) space from a direct mapping using associated meso-states’ particle identities with some misclassified interfacial particles. These classification uncertainties can be improved by a co-learning strategy which utilizes the probabilistic GM clustering and the information transfer between the structural space and configurational space iteratively until convergence. A final classification of meso-states in structural space and domains in configurational space are stable over long times and measured to have dynamical heterogeneities. Armed with such a classification protocol, various studies over the thermodynamic and dynamical properties of these domains indicate that the observed heterogeneity is the result of liquid–liquid phase separation after quenching to a supercooled state.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Exciting DeePMD: Learning excited-state energies, forces, and non-adiabatic couplings

We extend the DeePMD neural network architecture to predict electronic structure properties necessary to perform non-adiabatic dynamics simulations. While learning the excited state energies and forces follows a straightforward extension of the DeePMD approach for ground-state energies and forces, how to learn the map between the non-adiabatic coupling vectors (NACV) and the local chemical environment descriptors of DeePMD is less trivial. Most implementations of machine-learning-based non-adiabatic dynamics inherently approximate the NACVs, with an underlying assumption that the energy-difference-scaled NACVs are conservative fields. We overcome this approximation, implementing the method recently introduced by Richardson [J. Chem. Phys. 158, 011102 (2023)], which learns the symmetric dyad of the energy-difference-scaled NACV. Furthermore, the efficiency and accuracy of our neural network architecture are demonstrated through the example of the methaniminium cation CH 2 NH 2 + .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Online Anomaly Detection Using Machine Learning and HPC for Power System Synchrophasor Measurements

This paper presents an online early anomaly detection framework for phasor measurement units (PMUs) to monitor the power system dynamics and help prevent blackouts using machine learning approaches. Dynamical machine learning solutions including state space model and Kalman filter are conducted in this study to learn the nonlinear and nonstationary PMU measurements and accurately predict system behaviors in real-time. The anomalies can be detected within seconds by comparing the predicted system behaviors with the real system observations. The method proposed in this framework trains PMU data with a given time window (e.g., 5 seconds) using a dynamic nonlinear model, and then predicts system behaviors during the following time window. High prediction accuracy is achieved by applying the dynamic nonlinear model to the real-world PMU measurements – the anomalies detected are successfully validated given the recorded real-world events. High-performance-computing (HPC) techniques are utilized to further reduce computational time to provide real time power system situational awareness.

Ren, Huiying↗

Data-Driven Learning for the Mori--Zwanzig Formalism: A Generalization of the Koopman Learning Framework

A theoretical framework which unifies the conventional Mori--Zwanzig formalism and the approximate Koopman learning of deterministic dynamical systems from noiseless observation is presented. In this framework, the Mori--Zwanzig formalism, developed in statistical mechanics to tackle the hard problem of construction of reduced-order dynamics for high-dimensional dynamical systems, can be considered as a natural generalization of the Koopman description of the dynamical system. We next show that, similar to the approximate Koopman learning methods, data-driven methods can be developed for the Mori--Zwanzig formalism with Mori's linear projection operator. We have developed two algorithms to extract the key operators, the Markov and the memory kernel, using time series of a reduced set of observables in a dynamical system. We have adopted the Lorenz `96 system as a test problem and solved for the above operators. These operators exhibit complex behaviors, which are unlikely to be captured by traditional modeling approaches in Mori--Zwanzig analysis. The nontrivial generalized fluctuation-dissipation relationship, which relates the memory kernel with the two-time correlation statistics of the orthogonal dynamics, was numerically verified as a validation of the solved operators. Here we present numerical evidence that the generalized Langevin equation, a key construct in the Mori--Zwanzig formalism, is more advantageous in predicting the evolution of the reduced set of observables than the conventional approximate Koopman operators.

97 MATHEMATICS AND COMPUTING↗

Sharing is caring: An extensive analysis of parameter-based transfer learning for the prediction of building thermal dynamics

In recent years deep neural networks have been proposed as a lightweight data-driven model to capture high-dimensional, nonlinear physical processes to predict building thermal responses. However, the need of a large amount of data for the training process of deep neural networks clashes with the potential limited data availability in most existing or new buildings. Transfer learning aims to enhance the performance of a target learner exploiting knowledge from related and similar environments. This study conducted a suite of experiments that leveraged 250 data-driven models based on a synthetic dataset of a building archetype to study the influence of data availability, energy efficiency level, occupancy and climate for the transfer process of thermal dynamics. The performance of the transfer learning process was compared against a classical machine learning approach. Here, the results suggest that building thermal dynamics can be effectively transferred under the same climatic conditions, increasing performance when dealing with different occupancy schedules, efficiency levels and low data availability. Furthermore, the paper compares the performance of both transfer learning and machine learning approaches in an online fashion, to support the implementation in real-world deployment.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Reduced-order autodifferentiable ensemble Kalman filters

This paper introduces a computational framework to reconstruct and forecast a partially observed state that evolves according to an unknown or expensive-to-simulate dynamical system. Our reduced-order autodifferentiable ensemble Kalman filters (ROAD-EnKFs) learn a latent low-dimensional surrogate model for the dynamics and a decoder that maps from the latent space to the state space. The learned dynamics and decoder are then used within an EnKF to reconstruct and forecast the state. Numerical experiments show that if the state dynamics exhibit a hidden low-dimensional structure, ROAD-EnKFs achieve higher accuracy at lower computational cost compared to existing methods. If such structure is not expressed in the latent state dynamics, ROAD-EnKFs achieve similar accuracy at lower cost, making them a promising approach for surrogate state reconstruction and forecasting.

Mathematics↗

Predicting images for the dynamics of stellar clusters ( π-DOC ): a deep learning framework to predict mass, distance, and age of globular clusters

ABSTRACT Dynamical mass estimates of simple systems such as globular clusters (GCs) still suffer from up to a factor of 2 uncertainty. This is primarily due to the oversimplifications of standard dynamical models that often neglect the effects of the long-term evolution of GCs. Here, we introduce a new approach to measure the dynamical properties of GCs, based on the combination of a deep-learning framework and the large amount of data from direct N-body simulations. Our algorithm, π-DOC (Predicting Images for the Dynamics Of stellar Clusters) is composed of two convolutional networks, trained to learn the non-trivial transformation between an observed GC luminosity map and its associated mass distribution, age, and distance. The training set is made of V-band luminosity and mass maps constructed as mock observations from N-body simulations. The tests on π-DOC demonstrate that we can predict the mass distribution with a mean error per pixel of 27 per cent, and the age and distance with an accuracy of 1.5 Gyr and 6 kpc, respectively. In turn, we recover the shape of the mass-to-light profile and its global value with a mean error of 12 per cent, which implies that we efficiently trace mass segregation. A preliminary comparison with observations indicates that our algorithm is able to predict the dynamical properties of GCs within the limits of the training set. These encouraging results demonstrate that our deep-learning framework and its forward modelling approach can offer a rapid and adaptable tool competitive with standard dynamical models.

Chardin, Jonathan↗

Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics

Here, we propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. Conversely, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. Furthermore, we describe a framework in this work that paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structured Neural Network Modeling for Developing Digital Twins Models of Hydropower Generation Units

Dynamic modeling is a key part in the development of digital twin (DT) for dynamic systems. This is true for hydropower systems, where whole system modeling including penstock, turbine and generators, etc is important in realizing actuate modeling for the real systems. On the other hand, in response to the large variations of the power demand due to increased penetration of renewables such as wind and solar, hydropower systems are now required to operate in a large power generation range. This situation triggers the nonlinear characteristics of the generation unit with respect to its models. As such, it is imperative to use data driven modeling such as neural networks to learn the nonlinear dynamics of the hydropower generation unit. To achieve this objective, this study constructs a modeling and learning algorithm integrated with multiple structured neural network models for the modeling of turbine shaft speed, penstock pressure, and generator power output based on the generator power control setpoint, field current, and field voltage. In addition, the study uses the hydropower data from Tacoma Public Utilities to train and validate the proposed neural network algorithm. The results have shown that this structured neural network modeling approach can learn the system dynamics effectively by using the real-time data collected from the hydropower system with the desired modeling results.

Wang, Hong↗

Machine-Learned Committor Functions for Reactive Molecular Dynamics

Reactive molecular dynamics (MD) is a powerful tool for atomistic-scale modeling of a diverse range of chemical processes. However, scaling these simulations to large systems and long times scales remains a challenge because of the complexity of the potential energy function required. The authors previously developed a heuristic approach, called REACTER, that incorporates reactivity in MD simulations in a less general but much more computationally efficient manner. REACTER uses standard, fixed valence force fields as the underlying potentialenergy surface for describing all interatomic interactions but adds a procedure for enforcing user-defined reactions that occur when certain geometric constraints on relative atomic positions are satisfied. Further, these bonding changes can be accepted or rejected with a probability related tothe local thermal energy. This work seeks to generalize this approach by replacing the set of user defined geometric constraints and energetic criteria with a committor function that specifies the probability of a reaction occurring on the basis of the local atomic configuration. The committor function is a useful mathematical tool for modeling rare events but, unfortunately, is very difficult to compute for realistic systems in a general way. This work describes a method for approximating the committor function using a machine learning approach, specifically a deep neural network trained with data from reactive MD and DFT-based dynamics simulations. This network is coupled to the existing REACTER protocol, as implemented in the LAMMPS MD package, and used to make on-the-fly predictions of reaction probabilities without the more extensive user input previously required. The new method is demonstrated using the polymerization of polystyrene as a case study. Although very dependent on the quality and quantity of training data, machine-learned committor functions show promise as a method for incorporating reaction probability from higher level calculations into highly scalable MD simulations.

polymer simulations↗

Unraveling Hidden Order and Dynamics in a Heterogeneous Ferroelectric System Using Machine Learning

We uploaded two batches of datasets: Batch-a) Equilibrium dynamics at a constant temperature at zero electric-field, with one trajectory each for 4-different defect structures (i.e. SETs 1 to 4). Each trajectory has a time-step of 0.25 fs, and is run for 7775000 time-steps, with snapshots written out every 4 time-steps (i.e. every 1fs); and Batch-b) Non-Equilibrium dynamics at a constant temperature with the same 0.25 fs time-step, but data dumped every 500 times-steps (i.e. every 125fs) for each of the SETs. The total trajectory of each defect structure (i.e. each SETs 1 to 4) is 2800000 time-steps (5600 snapshots), with stepping of electric-field by 0.01 V/Ã…, after every 100,000 time-steps (i.e. every 200 snapshots), from E=0 to E=0.05 V/Ã… to E = -0.05 V/Ã… to E=0.05 V/Ã….

36 MATERIALS SCIENCE↗

Accelerating amorphous polymer electrolyte screening by learning to reduce errors in molecular dynamics simulated properties

Polymer electrolytes are promising candidates for the next generation lithium-ion battery technology. Large scale screening of polymer electrolytes is hindered by the significant cost of molecular dynamics (MD) simulation in amorphous systems: the amorphous structure of polymers requires multiple, repeated sampling to reduce noise and the slow relaxation requires long simulation time for convergence. Here, we accelerate the screening with a multi-task graph neural network that learns from a large amount of noisy, unconverged, short MD data and a small number of converged, long MD data. We achieve accurate predictions of 4 different converged properties and screen a space of 6247 polymers that is orders of magnitude larger than previous computational studies. Further, we extract several design principles for polymer electrolytes and provide an open dataset for the community. Our approach could be applicable to a broad class of material discovery problems that involve the simulation of complex, amorphous materials.

36 MATERIALS SCIENCE↗

Data-Driven Modeling and Correction of Vehicle Dynamics

We develop a data-driven framework for learning and correcting nonautonomous vehicle dynamics. Physics-based vehicle models are often simplified for tractability and therefore exhibit inherent model-form uncertainty, motivating the need for data-driven correction. Moreover, nonautonomous dynamics are governed by time-dependent control inputs, which pose challenges in learning predictive models directly from temporal snapshot data. To address these, we reformulate the vehicle dynamics via a local parameterization of the time-dependent inputs, yielding a modified system composed ofa sequence of local parametric dynamical systems. Here, we approximate these parametric systems using two complementary approaches. First, we employ the dimension reduction and interpolation in parameter space (DRIPS) methodology to construct efficient linear surrogate models, equipped with lifted observable spaces and manifold-based operator interpolation. This enables data-efficient learning of vehicle models whose dynamics admit accurate linear representations in the lifted spaces. Second, for more strongly nonlinear systems, we employ flow map learning (FML), a deep neural network (DNN) approach that approximates the parametric evolution map without requiring special treatment of nonlinearities. We further extend FML with a transfer-learning-based model correction procedure, enabling the correction of misspecified prior models using only a sparse set of high-fidelity or experimental measurements, without assuming a prescribed form for the correction term. Through a suite of numerical experiments on unicycle, simplified bicycle, and slip-based bicycle models, we demonstrate that DRIPS offers robust and highly data-efficient learning of nonautonomous vehicle dynamics, while FML provides expressive nonlinear modeling and effective correction of model-form errors under severe data scarcity.

data-driven modeling↗

Physics vs structure: A systematic benchmark of learning strategies for multi-zone building thermal dynamics

Recent advances in physics-informed and data-driven machine learning promise improved thermal models for advanced building control, yet there is limited quantitative evidence on when added physics structure and architectural complexity are beneficial. Here, this work presents a systematic benchmark of five representative system identification methods for modeling multi-zone building thermal dynamics: linear state-space models, multi-layer perceptrons, neural state-space models, neural ordinary differential equations, and physically-consistent neural networks. The methods are evaluated across multiple data regimes and zone coupling strategies. Using a high-fidelity multi-zone commercial building emulator, we examine short-term and long-term prediction accuracy, computational efficiency, and ease of development. Our results reveal critical trade-offs between prediction performance, model complexity, and physical consistency. We demonstrate that decoupled, nonlinear black-box models consistently outperform coupled physics-constrained architectures in both predictive accuracy and out-of-distribution robustness in majority of the test cases for the building type considered in the study. Our findings quantify the cost of complexity in building thermal modeling and provide concrete, actionable, scenario-based guidelines for selecting model classes for control-oriented applications.

Building thermal modeling↗