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At least 235 records · Page 13

Direct model reference adaptive control of robotic arms

The results of controlling A PUMA 560 Robotic Manipulator and the NASA shuttle Remote Manipulator System (RMS) using a Command Generator Tracker (CGT) based Model Reference Adaptive Controller (DMRAC) are presented. Initially, the DMRAC algorithm was run in simulation using a detailed dynamic model of the PUMA 560. The algorithm was tuned on the simulation and then used to control the manipulator using minimum jerk trajectories as the desired reference inputs. The ability to track a trajectory in the presence of load changes was also investigated in the simulation. Satisfactory performance was achieved in both simulation and on the actual robot. The obtained responses showed that the algorithm was robust in the presence of sudden load changes. Because these results indicate that the DMRAC algorithm can indeed be successfully applied to the control of robotic manipulators, additional testing was performed to validate the applicability of DMRAC to simulated dynamics of the shuttle RMS.

Kaufman, Howard↗

Mobile Thread Task Manager

The Mobile Thread Task Manager (MTTM) is being applied to parallelizing existing flight software to understand the benefits and to develop new techniques and architectural concepts for adapting software to multicore architectures. It allocates and load-balances tasks for a group of threads that migrate across processors to improve cache performance. In order to balance-load across threads, the MTTM augments a basic map-reduce strategy to draw jobs from a global queue. In a multicore processor, memory may be "homed" to the cache of a specific processor and must be accessed from that processor. The MTTB architecture wraps access to data with thread management to move threads to the home processor for that data so that the computation follows the data in an attempt to avoid L2 cache misses. Cache homing is also handled by a memory manager that translates identifiers to processor IDs where the data will be homed (according to rules defined by the user). The user can also specify the number of threads and processors separately, which is important for tuning performance for different patterns of computation and memory access. MTTM efficiently processes tasks in parallel on a multiprocessor computer. It also provides an interface to make it easier to adapt existing software to a multiprocessor environment.

Clement, Bradley J.↗

Large language models generate functional protein sequences across diverse families

Deep-learning language models have shown promise in various biotechnological applications, including protein design and engineering. Here, in this paper, we describe ProGen, a language model that can generate protein sequences with a predictable function across large protein families, akin to generating grammatically and semantically correct natural language sentences on diverse topics. The model was trained on 280 million protein sequences from >19,000 families and is augmented with control tags specifying protein properties. ProGen can be further fine-tuned to curated sequences and tags to improve controllable generation performance of proteins from families with sufficient homologous samples. Artificial proteins fine-tuned to five distinct lysozyme families showed similar catalytic efficiencies as natural lysozymes, with sequence identity to natural proteins as low as 31.4%. ProGen is readily adapted to diverse protein families, as we demonstrate with chorismate mutase and malate dehydrogenase.

59 BASIC BIOLOGICAL SCIENCES↗

Hybrid Active-Passive Systems for Control of Aircraft Interior Noise

Previous work has demonstrated the large potential for hybrid active-passive systems for attenuating interior noise in aircraft fuselages. The main advantage of an active-passive system is, by utilizing the natural dynamics of the actuator system, the control actuator power and weight is markedly reduced and stability/robustness is enhanced. Three different active-passive approaches were studied in the past year. The first technique utilizes multiple tunable vibration absorbers (ATVA) for reducing narrow band sound radiated from panels and transmitted through fuselage structures. The focus is on reducing interior noise due to propeller or turbo fan harmonic excitation. Two types of tunable vibration absorbers were investigated; a solid state system based upon a piezoelectric mechanical exciter and an electromechanical system based upon a Motran shaker. Both of these systems utilize a mass-spring dynamic effect to maximize tile output force near resonance of the shaker system and so can also be used as vibration absorbers. The dynamic properties of the absorbers (i.e. resonance frequency) were modified using a feedback signal from an accelerometer mounted on the active mass, passed through a compensator and fed into the drive component of the shaker system (piezoelectric element or voice coil respectively). The feedback loop consisted of a two coefficient FIR filter, implemented on a DSP, where the input is acceleration of tile ATVA mass and the output is a force acting in parallel with the stiffness of the absorber. By separating the feedback signal into real and imaginary components, the effective natural frequency and damping of the ATVA can be altered independently. This approach gave control of the resonance frequencies while also allowing the simultaneous removal of damping from the ATVA, thus increasing the ease of controllability and effectiveness. In order to obtain a "tuned" vibration absorber the chosen resonant frequency was set to the excitation frequency. In order to minimize sound radiation a gradient descent algorithm was developed which globally adapted the resonance frequencies of multiple ATVA's while minimizing a cost based upon the radiated sound power or sound energy obtained from an array of microphones.

Fuller, Chris R.↗

Knowledge Oriented Graph Unified Transformer (KOGUT) v0.1

KOGUT — Knowledge Oriented Graph Unified Transformer KOGUT implements the Relational Graph Transformer (RelGT) architecture for knowledge graph link prediction in biological domains, with a primary focus on microbial growth media prediction. While the original RelGT (arXiv:2505.10960) targets relational tables, time series, and multi-table databases, KOGUT adapts this architecture for heterogeneous biological knowledge graphs, providing first-in-class AI predictive models for microbial cultivation. Key Adaptations Beyond Original RelGT: - Knowledge Graph Focus: Applied to biological KGs with semantic node types (taxa, chemicals, media, phenotypes, environments) versus generic relational database tables, trained on the KG-Microbe knowledge graph (1.3M entities, 2.9M edges, 24 relation types). - Multimodal Node Encoding: Integrates node labels, categories, descriptions, and synonyms from KG metadata through learned embedding layers—adapting relational column features to graph node attributes with textual semantics. - Extended K-Hop Subgraph Strategy: Optimized neighborhood sampling (3-hop default, configurable up to 200 nodes) tuned for sparse biological networks, building on the original local-global attention framework with biological relation preservation. - Biolink Predicate Preservation: Type-specific transformations for 24 biological edge semantics (occurs_in, consumes, produces, has_phenotype, subclass_of) beyond standard relational foreign keys, enabling multi-relation link prediction. - Inductive Learning Support: Enables zero-shot predictions for novel taxa through feature-based embeddings (temperature, oxygen requirements, gram stain, cell shape), extending the original transductive relational benchmark scope to uncultured microorganisms. CheapSOTA Performance Optimizations (This Distribution): - VQ-EMA Centroid Attention: Vector quantization with exponential moving average for improved global context modeling (+5-10% MRR improvement). - HDF5 Precomputed Data Loading: One-time preprocessing of k-hop subgraphs to eliminate redundant graph traversals (2-5× training speedup). - Distributed Data Parallel Training: Multi-GPU support for scaling to larger knowledge graphs (tested on 4× NVIDIA A100 GPUs at NERSC Perlmutter). - Mixed Precision Training: Automatic mixed precision (AMP) for memory efficiency and faster training. Advantages Over Standard Knowledge Graph Embedding Models: Combines RelGT's proven multi-element tokenization (features, type, hop, structure) with graph-native biological representations, enabling interpretable link prediction across heterogeneous entities that standard embedding models (TransE, RotatE, ComplEx) and table-based transformers cannot directly model. Achieves near-perfect performance on microbial growth media prediction (MRR: 0.9966, Precision@1: 0.9932, Hit@10: 1.0000) while maintaining explainability through attention-based reasoning over biological pathways. Training Data: - KG-Microbe merged knowledge graph: 1,379,337 nodes, 2,960,472 edges - 24 biological relation types including taxonomic hierarchies, metabolic interactions, phenotype associations, and environmental relationships - Primary prediction task: Growth media suitability for microbial taxa (biolink:occurs_in, 50K edges) - Multi-relation capability: Predicts links for any of the 24 relation types, including chemical consumption/production, phenotype associations, and taxonomic classification Citation: Original RelGT Architecture: Dwivedi et al., "Relational Graph Transformer", arXiv:2505.10960, 2025 KOGUT Implementation: Knowledge Oriented Graph Unified Transformer for Microbial Growth Media Prediction Developed at Lawrence Berkeley National Laboratory (LBNL) Trained on NERSC Perlmutter supercomputer

Joachimiak, Marcin [Lawrence Berkeley National Lab↗

Progress Towards AIRS Science Team Version-7 at SRT

The AIRS Science Team Version-6 retrieval algorithm is currently producing level-3 Climate Data Records (CDRs) from AIRS that have been proven useful to scientists in understanding climate processes. CDRs are gridded level-3 products which include all cases passing AIRS Climate QC. SRT has made significant further improvements to AIRS Version-6. At the last Science Team Meeting, we described results using SRT AIRS Version-6.22. SRT Version-6.22 is now an official build at JPL called 6.2.4. Version-6.22 results are significantly improved compared to Version-6, especially with regard to water vapor and ozone profiles. We have adapted AIRS Version-6.22 to run with CrIS/ATMS, at the Sounder SIPS which processed CrIS/ATMS data for August 2014. JPL AIRS Version-6.22 uses the Version-6 AIRS tuning coefficients. AIRS Version-6.22 has at least two limitations which must be improved before finalization of Version-7: Version-6.22 total O3 has spurious high values in the presence of Saharan dust over the ocean; and Version-6.22 retrieved upper stratospheric temperatures are very poor in polar winter. SRT Version-6.28 addresses the first concern. John Blaisdell ran the analog of AIRS Version-6.28 in his own sandbox at JPL for the 14th and 15th of every month in 2014 and all of July and October for 2014. AIRS Version-6.28a is hot off the presses and addresses the second concern.

CrIS↗

An Adaptive Multiparameter Penalty Selection Method for Multiconstraint and Multiblock ADMM

This work presents a new method for online selection of multiple penalty parameters for the alternating direction method of multipliers (ADMM) algorithm applied to optimization problems with multiple constraints or functions with block matrix components. ADMM is widely used for solving constrained optimization problems in a variety of fields, including signal and image processing. Implementations of ADMM often utilize a single hyperparameter, referred to as the penalty parameter, which needs to be tuned to control the rate of convergence. However, in problems with multiple constraints, ADMM may demonstrate slow convergence regardless of penalty parameter selection due to scale differences between constraints. Accounting for scale differences between constraints to improve convergence in these cases requires introducing a penalty parameter for each constraint. The proposed method is able to adaptively account for differences in scale between constraints, providing robustness with respect to problem transformations and initial selection of penalty parameters. It is also simple to understand and implement. Our numerical experiments demonstrate that the proposed method performs favorably compared to a variety of existing penalty parameter selection methods.

97 MATHEMATICS AND COMPUTING↗

Unraveling Bacterial Adaptation Strategies in the Microbiome Shaped by the Chemical Environment of the Plant Rhizosphere

The rhizosphere is a dynamic environment where rhizodeposits that include primary and secondary metabolites and mucilage serve as nutrient sources for soil microorganisms, attracting them toward plant roots. However, understanding how these microbes specifically respond to plant root chemical signals has been hindered by the challenges of disentangling physical and chemical interactions between the microbes and plant roots. To address this, we implemented an innovative filter-based experimental setup on plant roots that creates a physical barrier while facilitating the exchange of chemical signals. The proteomic analysis of 10 Populus root-associated bacterial strains grown in the presence or absence of a plant in either individual or mixed community conditions provided detailed insights into the functional responses of these strains to the root chemical environment. Additionally, this approach allowed us to discern the impact of root exudates on overall community dynamics. In particular, metaproteomic analyses revealed that each of these 10 microbial members responds uniquely to the presence of the plant, with Bacillus and Pantoea exhibiting the most dramatic favorable impact. Proteomic examination revealed the details of metabolism fine-tuning, including processes such as chemotaxis and ATP-binding cassette transporter proteins. This study demonstrates the application of a filter-based experimental setup to study microbial responses to plant chemicals and sheds light on adaptation strategies employed by various bacterial strains for survival in the rhizosphere.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Learning-based CO 2 concentration prediction: Application to indoor air quality control using demand-controlled ventilation

There have been increasing concerns over the air quality inside buildings as high levels of bio-effluents can cause nausea, dizziness, headaches, and fatigue to the people working in those spaces. First published in 2004 as Standard 62.1, ASHRAE Standard 62.2-2019 requires highly occupied spaces to implement heating, ventilation, and air conditioning (HVAC) that can dilute contaminants produced by occupants. In this regard, occupant-centric ventilation control has been regarded as an effective practice to maintain a satisfactory indoor air quality (IAQ) when dealing with highly variable occupancy environments. However, few established models in current literature and practice consider dynamic occupancy behavior and adaptive IAQ control. To address this gap, a dynamic indoor CO2 model is constructed using machine learning algorithms to forecast CO2concentrations across a range of forecasting horizons. Herein, we tuned and compared six state-of-the-algorithms—including Support Vector Machine, Ada Boost, Random Forest, Gradient Boosting, Logistic Regression, and Multilayer Perceptron. The algorithms’ performances are validated using CO 2 and historical meteorological data collected from a campus classroom with a variable occupancy rate. Simulation results showed that Multilayer Perceptron can strongly predict the volatile CO 2 behavior and also outperforms other algorithms in terms of accuracy. Furthermore, a control strategy capable of modeling and detecting dynamic patterns of CO 2 level is utilized to modulate the ventilation rate in real-time and also reduce the energy consumption. The proposed controller reduced the HVAC fan’s energy consumption by 51.4% and provide ventilation as needed per the ASHRAE standards.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Modular Plasma Microreactor for Intensified Hydrogen Peroxide Production

Sustainable and decentralized manufacturing of hydrogen peroxide (H 2 O 2 ) has been extensively sought to replace the energy- and waste-intensive anthraquinone process. We introduce a helical biphasic microreactor in a coaxial dielectric barrier discharge (DBD) configuration as a modular, adaptable, and scalable intensified unit for H 2 O 2 production. Geometric and operating parameters such as electrode length, applied voltage, and gas and liquid flow rates can be tuned to regulate the residence time, delivered power, and gas–liquid interfacial area. In turn, these affect the key output parameters, i.e., H 2 O 2 concentration, production rate, and energy yield. We found a direct correlation between the H 2 O 2 production rate and the product of the interfacial area and residence time in the plasma region. We investigated the H 2 O 2 formation pathways using DMSO as an ·OH radical scavenger and found that H 2 O 2 forms by the dissolution of gaseous H 2 O 2 at low interfacial areas and is enhanced probably due to the interfacial recombination of ·OH radicals at a large gas–liquid interfacial area. The reactor temperature can also be externally controlled to intensify the production rate and energy yield of H 2 O 2 . Concentrations of up to 33 mM can be attained with a small footprint reactor that features a maximum energy yield of 4 g kWh –1 . Here, the plasma microreactor could epitomize a powerful process intensification tool for sustainable and distributed chemical manufacturing.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Adaptive Wavelength Scanning Lidar (AWSL) for 3D Mapping from Space

We present the design and performance of an adaptive wavelength scanning lidar (AWSL) for highly efficient mapping from low Earth orbit (LEO). Mapping is accomplished by steering a laser beam across 1,200 resolvable spots using wavelength tuning and grating dispersion. Any subset of these 1,200 spots can be selected by wavelength switching. The design is validated with an 1550-nm prototype using a fast wavelength-tuned (500-kHz) pulsed (2-ns) fiber laser with the beam dispersed by gratings for beam steering. Reflected pulses are detected with an eight-pixel detector array with single-photon sensitivity. Eight lidar returns are time-multiplexed to one output that is digitized with a single 1-GSPS-digitizer, to save power. A grating spectrometer rejects solar background noise spatially and spectrally, and images laser footprints on to the detector array. The gratings retain the fiber laser beam quality. We are developing a 1030-nm AWSL intended for a LEO SmallSat platform.

Guangning Yang↗

QMMM 2023: A program for combined quantum mechanical and molecular mechanical modeling and simulations

Combined quantum mechanical and molecular mechanical (QM/MM) methods play an important role in multiscale modeling and simulations. QMMM 2023 is a general-purpose program for single-point calculations, geometry optimizations, transition-state optimizations, and molecular dynamics (MD) at the QM/MM level. It calls a QM package and an MM package to perform the required single-level calculations and combines them into a QM/MM energy by a variety of schemes. QMMM 2023 supports GAMESS-US, Gaussian, and ORCA as QM packages and Tinker as the MM package. Four types of treatments are available for embedding the QM subsystem in the MM environment: mechanical embedding with gas-phase calculations of the QM region, electronic embedding that allows polarization of the QM region by the MM environment, polarizable embedding for mutual polarization of the QM and MM regions, and flexible embedding for both mutual polarization and partial charge transfer between the QM and MM regions. Boundaries between QM and MM regions that pass through covalent bonds can be treated by several methods, including the redistributed charge (RC) scheme, redistributed charge and dipole (RCD) scheme, balanced-RC scheme, balanced-RCD scheme, screened charge scheme that takes account of charge penetration effects, and smeared charge scheme that delocalizes the MM charges near the QM–MM boundary. Geometry optimization can be done using the optimizer implemented in QMMM 2023 or the Berny optimizer in Gaussian through external calls to Gaussian. Molecular dynamics simulations can be performed at the pure-MM level, pure-QM level, fixed-partitioning QM/MM level, and adaptive-partitioning QM/MM level. As a result, the adaptive-partitioning treatments permit on-the-fly relocation of the QM–MM boundary by dynamically reclassifying atoms or groups into the QM or MM subsystems.

97 MATHEMATICS AND COMPUTING↗

Slimmer Geminals For Accurate F12 Electronic Structure Models

The Slater-type F12 geminal length scales originally tuned for the second-order Mo̷ller-Plesset F12 method are too large for higher-order F12 methods formulated using the SP (diagonal fixed-coefficient spin-adapted) F12 ansatz. The new geminal parameters reported herein reduce the basis set incompleteness errors (BSIEs) of absolute coupled-cluster singles and doubles F12 correlation energies by a significant─and increase with the cardinal number of the basis─margin. The effect of geminal reoptimization is especially pronounced for the cc-pVXZ-F12 basis sets (specifically designed for use with F12 methods) relative to their conventional aug-cc-pVXZ counterparts. The BSIEs of relative energies are less affected, but substantial reductions can be obtained, especially for atomization energies and ionization potentials with the cc-pVXZ-F12 basis sets. The new geminal parameters are therefore recommended for all applications of high-order F12 methods, such as coupled-cluster F12 methods and transcorrelated F12 methods.

Powell, Samuel R. [Virginia Polytechnic Inst. and ↗

Long-Term Statistical Process Monitoring of an Ultrafiltration Water Treatment Process

As water treatment technology has improved, the amount of available process data has substantially increased, making real-time, data-driven fault detection a reality. One shortcoming of the fault detection literature is that methods are usually evaluated by comparing their performance on hand-picked, short-term case studies, which yields no insight into long-term performance. In this work, we first evaluate multiple statistical and machine learning approaches for detrending process data. Then, we evaluate the performance of a PCA-based fault detection approach, applied to the detrended data, to monitor influent water quality, filtrate quality, and membrane fouling of an ultrafiltration membrane system for indirect potable reuse. Based on two short case studies, the adaptive lasso detrending method is selected, and the performance of the multivariate approach is evaluated over more than a year. The method is tested for different sets of three critical tuning parameters, and we find that for long-term, autonomous monitoring to be successful, these parameters should be carefully evaluated. However, in comparison with industry standards of simpler, univariate monitoring or daily pressure decay tests, multivariate monitoring produces substantial benefits in long-term testing.

ammonia↗

Estimating and Calibrating DER Model Parameters Using Levenberg–Marquardt Algorithm in Renewable Rich Power Grid

The proliferation of inverter-based distributed energy resources (IBDERs) has increased the number of control variables and dynamic interactions, leading to new grid control challenges. For stability analysis and designing appropriate protection controls, it is important that IBDER models are accurate. This paper focuses on the accurate estimation and parameter calibration of DER_A, a recently proposed aggregated IBDER model. In particular, we focus on the parameters of the reactive power–voltage regulation module. We formulate the problem of parameter tuning as a non-linear least square minimization problem and solve it using the Levenberg–Marquardt (LM) method. The LM method is primarily chosen due to its flexibility in adaptively selecting between the steepest descent and Gauss–Newton methods through a damping parameter. The LM approach is used to minimize the error between the actual measurements and the estimated response of the model. Further, the computational challenges posed by the numerical calculation of the Jacobian are tackled using a quasi-Newton root-finding approach. The proposed method is validated on a real feeder model in the northeastern part of the United States. The feeder is modeled in OpenDSS and the measurements thus obtained are fed to the DER_A model for calibration. The simulation results indicate that our approach is able to successfully calibrate the relevant model parameters quickly and with high accuracy, with a total sum of square error of 3.57 × 10 –7 .

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance

The success of Mycobacterium tuberculosis (Mtb) is largely attributed to its ability to physiologically adapt and withstand diverse localized stresses within host microenvironments. Here, we present a data-driven model (EGRIN 2.0) that captures the dynamic interplay of environmental cues and genome-encoded regulatory programs in Mtb. Analysis of EGRIN 2.0 shows how modulation of the MtrAB two-component signaling system tunes Mtb growth in response to related host microenvironmental cues. Disruption of MtrAB by tunable CRISPR interference confirms that the signaling system regulates multiple peptidoglycan hydrolases, among other targets, that are important for cell division. Further, MtrA decreases the effectiveness of antibiotics by mechanisms of both intrinsic resistance and drug tolerance. Together, the model-enabled dissection of complex MtrA regulation highlights its importance as a drug target and illustrates how EGRIN 2.0 facilitates discovery and mechanistic characterization of Mtb adaptation to specific host microenvironments within the host.

59 BASIC BIOLOGICAL SCIENCES↗

Learning high-dimensional parametric maps via reduced basis adaptive residual networks

We propose a scalable framework for the learning of high-dimensional parametric maps via adaptively constructed residual network (ResNet) maps between reduced bases of the inputs and outputs. When just few training data are available, it is beneficial to have a compact parametrization in order to ameliorate the ill-posedness of the neural network training problem. By linearly restricting high-dimensional maps to informed reduced bases of the inputs, one can compress high-dimensional maps in a constructive way that can be used to detect appropriate basis ranks, equipped with rigorous error estimates. A scalable neural network learning framework is thus to learn the nonlinear compressed reduced basis mapping. Unlike the reduced basis construction, however, neural network constructions are not guaranteed to reduce errors by adding representation power, making it difficult to achieve good practical performance. Inspired by recent approximation theory that connects ResNets to sequential minimizing flows, we present an adaptive ResNet construction algorithm. This algorithm allows for depth-wise enrichment of the neural network approximation, in a manner that can achieve good practical performance by first training a shallow network and then adapting. We prove universal approximation of the associated neural network class for $L^2_v$ functions on compact sets. Our overall framework allows for constructive means to detect appropriate breadth and depth, and related compact parametrizations of neural networks, significantly reducing the need for architectural hyperparameter tuning. Numerical experiments for parametric PDE problems and a 3D CFD wing design optimization parametric map demonstrate that the proposed methodology can achieve remarkably high accuracy for limited training data, and outperformed other neural network strategies we compared against.

42 ENGINEERING↗

Application of a Constant Gain Extended Kalman Filter for In-Flight Estimation of Aircraft Engine Performance Parameters

An approach based on the Constant Gain Extended Kalman Filter (CGEKF) technique is investigated for the in-flight estimation of non-measurable performance parameters of aircraft engines. Performance parameters, such as thrust and stall margins, provide crucial information for operating an aircraft engine in a safe and efficient manner, but they cannot be directly measured during flight. A technique to accurately estimate these parameters is, therefore, essential for further enhancement of engine operation. In this paper, a CGEKF is developed by combining an on-board engine model and a single Kalman gain matrix. In order to make the on-board engine model adaptive to the real engine s performance variations due to degradation or anomalies, the CGEKF is designed with the ability to adjust its performance through the adjustment of artificial parameters called tuning parameters. With this design approach, the CGEKF can maintain accurate estimation performance when it is applied to aircraft engines at offnominal conditions. The performance of the CGEKF is evaluated in a simulation environment using numerous component degradation and fault scenarios at multiple operating conditions.

Kobayashi, Takahisa↗