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At least 523 records · Page 29

MACAW v1.0

The ability to embed molecules in a numeric space is essential in order to build mathematical and machine-learning models describing molecular properties or other processes affected by molecules. MACAW is a cheminformatic tool that allows embedding small molecules into a multidimensional numeric space. In the embedding, each molecule is assigned a numeric vector that captures information of the molecule in relation to other molecules, and that vector can be used as input to mathematical models. Molecules that are more similar to each other are embedded closer in this numeric space, whereas molecules that are more different are embedded further away. One advantage of the MACAW embedding technology compared to established alterantives is that it is fast and does not require extensive computational resources or expertise. In particular, MACAW embeddings can be used as input to mathematical models without the need for variable cleaning or feature selection, saving time and simplifying their use. On the other hand, MACAW also contains methods to generate new molecules and to recommend new molecules satisfying a desired molecular property. The generation of new molecules can be biased based on an input set of molecules, effectively generating molecular diversity around it. In its turn, MACAW's molecular recommendation tool is a novel method for evolving molecules in silico towards a desired molecular specification. In this method, the biased molecular generator tool is applied iteratively in combination with a molecular selection step. As a result, in each iteration the molecules selected by the software are increasingly closer to the desired specification. Both the molecular generation and the molecular recommendation tools are very fast, efficient, and intuitive to use.

Roger, VincentBlay↗

Open-Source Steady-State Models for Integration of Wave Energy Converter into Microgrids

This paper proposes a software framework, WEC-Grid, for integrating wave energy converters (WECs) into power flow software, such as Siemens PSS®E, to aid the integration of alternative energy sources into Microgrids. While integrating alternative sources such as WECs presents specific challenges such as cost, power quality, and power variability, wave energy is a promising renewable energy resource. Evaluating the integration of WECs into the power grid is a complex and nuanced problem that requires seamless communication between a WEC model and power flow software. The presented WEC-Grid software framework bridges and extends the functionality of WEC-Sim, an open-source WEC modeling package for MATLAB, through a wave-to-wire (W2W) electro-mechanical power conversion and processing model. WEC-Grid acts as a software wrapper, handler, and communication layer between the W2W modeler and power flow software. The software is designed to represent each grid system as a class object, allowing power system operators to perform power system duties such as contingency planning and dispatch operations. The integration of WECs with PSS®E’s power flow calculations workflow is demonstrated with an IEEE RTS case study.

16 TIDAL AND WAVE POWER↗

HYPPO: A Surrogate-Based Multi-Level Parallelism Tool for Hyperparameter Optimization

We present a new software, HYPPO, that enables the automatic tuning of hyperparameters of various deep learning (DL) models. Unlike other hyperparameter optimization (HPO) methods, HYPPO uses adaptive surrogate models and directly accounts for uncertainty in model predictions to find accurate and reliable models that make robust predictions. Using asynchronous nested parallelism, we are able to significantly alleviate the computational burden of training complex architectures and quantifying the uncertainty. HYPPO is implemented in Python and can be used with both TensorFlow and PyTorch libraries. We demonstrate various software features on time-series prediction and image classification problems as well as a scientific application in computed tomography image reconstruction. Finally, we show that (1) we can reduce by an order of magnitude the number of evaluations necessary to find the most optimal region in the hyperparameter space and (2) we can reduce by two orders of magnitude the throughput for such HPO process to complete.

adaptation models↗

A novel physics-based and data-supported microstructure model for part-scale simulation of laser powder bed fusion of Ti-6Al-4V

The elasto-plastic material behavior, material strength and failure modes of metals fabricated by additive manufacturing technologies are significantly determined by the underlying process-specific microstructure evolution. In this work a novel physics-based and data-supported phenomenological microstructure model for Ti-6Al-4V is proposed that is suitable for the part-scale simulation of laser powder bed fusion processes. The model predicts spatially homogenized phase fractions of the most relevant microstructural species, namely the stable β-phase, the stable α s -phase as well as the metastable Martensite α m -phase, in a physically consistent manner. In particular, the modeled microstructure evolution, in form of diffusion-based and non-diffusional transformations, is a pure consequence of energy and mobility competitions among the different species, without the need for heuristic transformation criteria as often applied in existing models. The mathematically consistent formulation of the evolution equations in rate form renders the model suitable for the practically relevant scenario of temperature- or time-dependent diffusion coefficients, arbitrary temperature profiles, and multiple coexisting phases. Due to its physically motivated foundation, the proposed model requires only a minimal number of free parameters, which are determined in an inverse identification process considering a broad experimental data basis in form of time-temperature transformation diagrams. Subsequently, the predictive ability of the model is demonstrated by means of continuous cooling transformation diagrams, showing that experimentally observed characteristics such as critical cooling rates emerge naturally from the proposed microstructure model, instead of being enforced as heuristic transformation criteria. Eventually, the proposed model is exploited to predict the microstructure evolution for a realistic selective laser melting application scenario and for the cooling/quenching process of a Ti-6Al-4V cube of practically relevant size. Numerical results confirm experimental observations that Martensite is the dominating microstructure species in regimes of high cooling rates, e.g., due to highly localized heat sources or in near-surface domains, while a proper manipulation of the temperature field, e.g., by preheating the base-plate in selective laser melting, can suppress the formation of this metastable phase.

Inverse parameter identification↗

Predicting transport of intra-articularly injected growth factor fusion proteins into human knee joint cartilage

There are no drugs or treatment methods known to prevent the development of post-traumatic osteoarthritis (PTOA), a type of osteoarthritis (OA) that is triggered by traumatic joint injuries and accounts for ~12% of the nearly 600 million OA cases worldwide. Lack of effective drug delivery techniques remains a major challenge in developing clinically effective treatments, but cationic delivery carriers can help overcome this challenge. Scaling up treatments that are effective in in vitro models to achieve success in preclinical in vivo models and clinical trials is also a challenging problem in the field. Here we use a cationic green fluorescent protein (GFP) as a carrier to deliver Insulin-Like Growth Factor 1 (IGF-1), a drug considered as a potential therapeutic for PTOA. GFP-IGF-1 conjugates were first synthesized as fusion proteins with different polypeptide linkers, and their transport properties were characterized in human cartilage explants. In vitro experimental data were used to develop a predictive mathematical transport model that was validated using an independent in vitro experimental data set. In this study, the model was used to predict the transport of these fusion proteins upon intra-articular injection into human knee joints. The predictions included results for the rate and extent of fusion protein penetration into cartilage, and the maximum levels of fusion proteins that would escape into systemic circulation through the joint capsule. Together, our transport measurements and model set the stage for translation of such explant culture studies to in vivo preclinical studies and potentially clinical application.

36 MATERIALS SCIENCE↗

Hubbard-corrected oxide formation enthalpies without adjustable parameters

A density functional theory (DFT) approach to computing transition metal oxide heat of formation without adjustable parameters is presented. Different degrees of d-electron localization in oxides are treated within the DFT+U approach with site-dependent, first-principles Hubbard U-parameters obtained from linear response theory, and delocalized states in the metallic phases are treated without Hubbard corrections. Comparison of relative stabilities of these differently treated phases is enabled by a local d-electron density matrix-dependent model, which was found by genetic programming against experimental reference formation enthalpies. This mathematically simple model does not explicitly depend on the Hubbard-corrected ionic species and is shown to reproduce the heats of formation of the Mott insulators Ca 2 RuO 4 and Y 2 Ru 2 O 7 within ~3% of experimental results, where the experimental training data did not contain Ru oxides. This newly developed method thus absolves from the need for element-specific corrections fitted to experiments in existing Hubbard-corrected approaches to the prediction of reaction energies of transition metal oxides and metals. The absence of fitting parameters opens up here the possibility to predict relative thermodynamic stabilities and reaction energies involving d-states of varying degree of localization at transition metal oxide interfaces and defects, where site-dependent U-parameters will be particularly important and devising a fitting scheme against experimental data with predictive power would be exceedingly difficult.

transition metal oxides↗

Predictor-corrector models for lightweight massive machine-type communications in Industry 4.0

Future Industry 4.0 scenarios are characterized by seamless integration between computational and physical processes. To achieve this objective, dense platforms made of small sensing nodes and other resource constraint devices are ubiquitously deployed. All these devices have a limited number of computational resources, just enough to perform the simple operation they are in charge of. The remaining operations are delegated to powerful gateways that manage sensing nodes, but resources are never unlimited, and as more and more devices are deployed on Industry 4.0 platforms, gateways present more problems to handle massive machine-type communications. Although the problems are diverse, those related to security are especially critical. To enable sensing nodes to establish secure communications, several semiconductor companies are currently promoting a new generation of devices based on Physical Unclonable Functions, whose usage grows every year in many real industrial scenarios. Those hardware devices do not consume any computational resource but force the gateway to keep large key-value catalogues for each individual node. In this context, memory usage is not scalable and processing delays increase exponentially with each new node on the platform. In this paper, we address this challenge through predictor-corrector models, representing the key-value catalogues. Models are mathematically complex, but we argue that they consume less computational resources than current approaches. The lightweight models are based on complex functions managed as Laurent series, cubic spline interpolations, and Boolean functions also developed as series. Unknown parameters in these models are predicted, and eventually corrected to calculate the output value for each given key. The initial parameters are based on the Kane Yee formula. An experimental analysis and a performance evaluation are provided in the experimental section, showing that the proposed approach causes a significant reduction in the resource consumption.

97 MATHEMATICS AND COMPUTING↗

An unsupervised machine-learning checkpoint-restart algorithm using Gaussian mixtures for particle-in-cell simulations

We propose an unsupervised machine-learning checkpoint-restart (CR) algorithm for particle-in-cell (PIC) algorithms using Gaussian mixtures (GM). The algorithm compresses the particle population per spatial cell by constructing a velocity distribution function using GM. Particles are reconstructed at restart time by local resampling of the Gaussians. To guarantee fidelity of the CR process, we ensure the exact preservation of invariants such as charge, momentum, and energy for both compression and reconstruction stages, everywhere on the mesh. We also ensure the preservation of Gauss' law after particle reconstruction by exactly matching the density profile at restart time. As a result, the GM CR algorithm is shown to provide a clean, conservative restart capability while potentially affording orders of magnitude savings in input/output requirements. Here, we demonstrate the algorithm using a recently developed exactly energy- and charge-conserving PIC algorithm using both electrostatic and electromagnetic tests. The tests demonstrate not only a high-fidelity CR capability, but also its potential for enhancing the fidelity of the PIC solution for a given particle resolution.

97 MATHEMATICS AND COMPUTING↗

Modeling of nitrogen fixation and polymer production in the heterotrophic diazotroph Azotobacter vinelandii DJ

Nitrogen fixation is an important metabolic process carried out by microorganisms, which converts molecular nitrogen into inorganic nitrogenous compounds such as ammonia (NH 3 ). These nitrogenous compounds are crucial for biogeochemical cycles and for the synthesis of essential biomolecules, i.e. nucleic acids, amino acids and proteins. Azotobacter vinelandii is a bacterial non-photosynthetic model organism to study aerobic nitrogen fixation (diazotrophy) and hydrogen production. Moreover, the diazotroph can produce biopolymers like alginate and polyhydroxybutyrate (PHB) that have important industrial applications. However, many metabolic processes such as partitioning of carbon and nitrogen metabolism in A. vinelandii remain unknown to date. Genome-scale metabolic models (M-models) represent reliable tools to unravel and optimize metabolic functions at genome-scale. M-models are mathematical representations that contain information about genes, reactions, metabolites and their associations. M-models can simulate optimal reaction fluxes under a wide variety of conditions using experimentally determined constraints. Here we report on the development of a M-model of the wild type bacterium A. vinelandii DJ (iDT1278) which consists of 2,003 metabolites, 2,469 reactions, and 1,278 genes. We validated the model using high-throughput phenotypic and physiological data, testing 180 carbon sources and 95 nitrogen sources. iDT1278 was able to achieve an accuracy of 89% and 91% for growth with carbon sources and nitrogen source, respectively. This comprehensive M-model will help to comprehend metabolic processes associated with nitrogen fixation, ammonium assimilation, and production of organic nitrogen in an environmentally important microorganism.

59 BASIC BIOLOGICAL SCIENCES↗

Enhanced descriptor identification and mechanism understanding for catalytic activity using a data-driven framework: revealing the importance of interactions between elementary steps

We report accurate identification of descriptors for catalytic activities has long been essential to the in-depth understanding of catalysis and recently to set the basis for catalyst screening. However, commonly used methods suffer from low accuracy in predictability. This study reports an enhanced approach to accurately identify the descriptors from a kinetic dataset using a machine learning (ML) surrogate model. CO hydrogenation to methanol over Cu-based catalysts was taken as a case study. Our model captures not only the contribution from individual elementary steps but also the interaction between relevant steps within a reaction network, which was found to be essential for high accuracy. As a result, six effective descriptors are identified, which are accurate enough to ensure the trained gradient boosted regression (GBR) model for good prediction of the methanol turnover frequency (TOF) over metal (M)-doped Cu(111) model surfaces (M = Au, Cu, Pd, Pt, Ni). More importantly, going beyond the purely mathematical ML model, the catalytic role of each identified descriptor can be revealed by using model-agnostic interpretation tools, which enhances the insight into the promoting effect of alloying. The trained GBR model outperforms the conventional derivative-based methods in terms of both the predictability and the mechanism understanding. It opens alternative possibilities toward accurate descriptor-based rational catalyst optimization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Semi-Analytical Hierarchical Bayesian Inference of Nonlinear Model Structure in Stochastic Dynamics: Applied to Compartmental Models of Infectious Diseases

A Bayesian computational framework for parsimonious inference in stochastic nonlinear dynamical systems is presented. This framework enables the concurrent estimation of system states, time-varying parameters, time-invariant parameters, and the optimal sparsity structure of the model parameters. Because differential equation-based models are often simplified mechanistic or phenomenological representations, robust inference from noisy measurement data requires explicit treatment of model error and uncertainty. Model error and time-varying parameters can be represented as random processes, enabling inference while making minimal assumptions about the underlying sources of discrepancy and variability. Adopting stochastic differential equation representations affords the model significant flexibility, but can also render it susceptible to overfitting during statistical inversion, where the inferred model may track noise rather than the underlying signal. To alleviate the effects of overfitting and to enable the discovery of the optimal sparse representation of the time-invariant parameters, a Bayesian sparse learning algorithm is embedded within the framework. This sparse learning framework adopts an approximate hierarchical Bayesian setting defined by a series of semi-analytical expressions. The model structure inference framework is validated using a stochastic compartmental model for tracking and forecasting active cases of an infectious disease. Compartmental models describe population-level infectious disease dynamics through interactions among population fractions grouped by disease state. Mathematically, such models consist of a system of coupled ordinary differential equations. This example adopts an expressive compartmental model that includes multiple possible interactions between disease states, motivated by early uncertainty surrounding COVID-19 reinfection dynamics and their implications for long-term epidemic forecasting. The sparse learning exercise permits the inference of a priori unknown epidemiological dynamics from simulated public health data, discovering the nested compartmental model that optimizes the trade-off between average data-fit and model complexity. It is shown that inducing sparsity among the model parameters eliminates redundant interactions between compartments, equivalently revealing the optimal coupling structure between differential equations.

97 MATHEMATICS AND COMPUTING↗

AEOLUS: Advances in Experimental Design, Optimal Control, and Learning for Uncertain Complex Systems

Sustained advances in the mathematics of modeling and simulation have resulted in the capability today for routine simulation of a number of large scale complex DOE-relevant systems. As remarkable as this capability for solving the so-called forward problem is, it is typically only the first step-an inner loop within an outer loop that explores the simulation model's parameter space and decision space to characterize uncertainty in the model's predictions, learn unknown model parameters from data, design the most informative experiments, determine optimal control strategies, and create optimal designs. Broadly, what unifies all of these outer loop problems is that they are, in one form or another, optimization problems over parameter/control/design space that are constrained by complex uncertain models. To fully realize the power of scientific simulation as a basis for scientific discovery, technological innovation, and rational decision-making, it is imperative to move beyond simulation to tackle the outer loop of optimization for learning from data, experimental design, and control with complex uncertain models. When the models under consideration are large-scale and complex, and when the optimization variable and uncertain parameter spaces are high (or infinite) dimensional, this constitutes a grand challenge of the highest order, and is intractable with conventional methods. To overcome these challenges, the AEOLUS Center was established to develop a unified mathematical, computational, and statistical framework for (1) Learning predictive models from complex data via Bayesian inference and optimization, and (2) Optimizing experiments, processes, and designs using the resulting uncertain models. These problems are intractable with conventional methods, for several reasons: (1) The simulation problems that govern the inner loops of the optimization problems are expensive to execute (due to severe nonlinearity, heterogeneity, multiphysics/multiscale coupling); (2) The optimization variable and uncertain parameter spaces are high dimensional, often stemming from discretizations of infinite dimensional fields such as initial conditions, sources, or material properties. We argue that the key to overcoming these challenges is to develop new mathematical, computational, and statistical methods that exploit the structure of the Bayesian inference and optimization problems mediated by their underlying complex uncertain models. This structure includes the regularity, sparsity, geometry, low intrinsic dimensionality, and multifidelity nature of the maps from uncertain parameter/optimization variable spaces to the specific objectives targeted: Bayesian inference, optimal experimental design, and optimal control design. Black box methods developed as generic tools are incapable of exploiting this structure. To be successful, we must create, integrate, and cross-fertilize ideas across multiple areas of applied math--including approximation theory, Bayesian inference, data science, experimental design, information theory, machine learning, model reduction, optimal control theory, parallel algorithms, PDE-constrained optimization, randomized algorithms, stochastic optimization, and uncertainty quantification--all while exploiting the structure of the problems at hand. With this goal in mind, we have marshaled a team of leading authorities in these areas. While the methods we develop will be broadly applicable across a wide spectrum of DOE problems in which experiments inform models and the systems those models describe must be optimized under uncertainty, we have chosen a specific area, advanced manufacturing and materials, to drive our work. AMM is characterized by complex models across multiple scales, and is a rich source of challenging problems in inference, experimental design, and optimal control, requiring multifaceted and integrated advances in applied mathematics. As such, AMM serves as an excellent vehicle to motivate and demonstrate the advances in applied mathematics developed by our center.

97 MATHEMATICS AND COMPUTING↗

Machine learning unifies flexibility and efficiency of spinodal structure generation for stochastic biomaterial design

Abstract Porous biomaterials design for bone repair is still largely limited to regular structures (e.g. rod-based lattices), due to their easy parameterization and high controllability. The capability of designing stochastic structure can redefine the boundary of our explorable structure–property space for synthesizing next-generation biomaterials. We hereby propose a convolutional neural network (CNN) approach for efficient generation and design of spinodal structure—an intriguing structure with stochastic yet interconnected, smooth, and constant pore channel conducive to bio-transport. Our CNN-based approach simultaneously possesses the tremendous flexibility of physics-based model in generating various spinodal structures (e.g. periodic, anisotropic, gradient, and arbitrarily large ones) and comparable computational efficiency to mathematical approximation model. We thus successfully design spinodal bone structures with target anisotropic elasticity via high-throughput screening, and directly generate large spinodal orthopedic implants with desired gradient porosity. This work significantly advances stochastic biomaterials development by offering an optimal solution to spinodal structure generation and design.

59 BASIC BIOLOGICAL SCIENCES↗

Steady-State Analysis of Microgrid Distributed Control Under Denial of Service Attacks

Distributed control is an effective method to coordinate multiple components in a microgrid. It usually has mandatory requirements for communication graph topology; changing the topology unexpectedly could disrupt the operation of a distributed controller. A denial of service (DoS) attack blocks communication channels to cause variations in communication graph. Unforeseen topology changes render a controller to receive incomplete system information. Control decisions made based on incorrect information can lead to significantly reduced grid supporting capability. As a result, the vital power balance between generation and load may be challenged. Determining power balance requires steady-state power flow analysis; however, the cyber-induced steady-state analysis is not well studied in the literature. Here, in this article, we show that a cyber–physical microgrid with unknown DoS attacks has augmented uncertain power flow equations, whose special structure creates new computational issue to determining power balance. To deal with the issue, we develop a novel cyber-induced microgrid model: the cyber–physical system is transformed into a pure physical model, where the disruption effects of DoS in the cyber layer are shown to be equivalent to the variations of the physical model parameters. With the transformed system, we develop a sufficient condition to ascertain the system power balance under unknown DoS attacks. In addition, practical insights for resilient distributed control design are shown as well.

24 POWER TRANSMISSION AND DISTRIBUTION↗

A data-driven peridynamic continuum model for upscaling molecular dynamics

Nonlocal models, including peridynamics, often use integral operators that embed lengthscales in their definition. However, the integrands in these operators are difficult to define from the data that are typically available for a given physical system, such as laboratory mechanical property tests. In contrast, molecular dynamics (MD) does not require these integrands, but it suffers from computational limitations in the length and time scales it can address. To combine the strengths of both methods and to obtain a coarse-grained, homogenized continuum model that efficiently and accurately captures materials’ behavior, we propose a learning framework to extract, from MD data, an optimal Linear Peridynamic Solid (LPS) model as a surrogate for MD displacements. To maximize the accuracy of the learnt model we allow the peridynamic influence function to be partially negative, while preserving the well-posedness of the resulting model. To achieve this, we provide sufficient well-posedness conditions for discretized LPS models with sign-changing influence functions and develop a constrained optimization algorithm that minimizes the equation residual while enforcing such solvability conditions. This framework guarantees that the resulting model is mathematically well-posed, physically consistent, and that it generalizes well to settings that are different from the ones used during training. We illustrate the efficacy of the proposed approach with several numerical tests for single layer graphene. Our two-dimensional tests show the robustness of the proposed algorithm on validation data sets that include thermal noise, different domain shapes and external loadings, and discretizations substantially different from the ones used for training.

homogenization↗

On closures for reduced order models - A spectrum of first-principle to machine-learned avenues

For over a century, reduced order models (ROMs) have been a fundamental discipline of theoretical fluid mechanics. Early examples include Galerkin models inspired by the Orr–Sommerfeld stability equation and numerous vortex models, of which the von Karman vortex street is one of the most prominent. Subsequent ROMs typically relied on first principles, like mathematical Galerkin models, weakly nonlinear stability theory, and two- and three-dimensional vortex models pioneered the data-driven proper orthogonal decomposition (POD) modeling. In early POD modeling, available data were used to build an optimal basis, which was then utilized in a classical Galerkin procedure to construct the ROM, but data have made a profound impact on ROMs beyond the Galerkin expansion. In this paper, we take a modest step and illustrate the impact of data-driven modeling on one significant ROM area. Specifically, we focus on ROM closures, which are correction terms that are added to the classical ROMs in order to model the effect of the discarded ROM modes in under-resolved simulations. Through simple examples, we illustrate the main modeling principles used to construct the classical ROMs, motivate and introduce modern ROM closures, and show how data-driven modeling, artificial intelligence, and machine learning have changed the standard ROM methodology over the last two decades. Finally, we outline our vision on how the state-of-the-art data-driven modeling can continue to reshape the field of reduced order modeling.

42 ENGINEERING↗

Approximating Nash Equilibrium in Day-ahead Electricity Market Bidding with Multi-agent Deep Reinforcement Learning

In this paper, a day-ahead electricity market bidding problem with multiple strategic generation company (GEN-CO) bidders is studied. The problem is formulated as a Markov game model, where GENCO bidders interact with each other todevelop their optimal day-ahead bidding strategies. Considering unobservable information in the problem, a model-free and data-driven approach, known as multi-agent deep deterministic policy gradient (MADDPG), is applied for approximating the Nash equilibrium (NE) in the above Markov game. The MADDPG algorithm has the advantage of generalization due to the automatic feature extraction ability of the deep neural networks. The algorithm is tested on an IEEE 30-bus system with three competitive GENCO bidders in both an uncongested caseand a congested case. Comparisons with a truthful bidding strategy and state-of-the-art deep reinforcement learning methods including deep Q network and deep deterministic policy gradient (DDPG) demonstrate that the applied MADDPG algorithm can find a superior bidding strategy for all the market participants with increased profit gains. In addition, the comparison with a conventional model-based method shows that the MADDPG algorithm has higher computational efficiency, which is feasible for real-world applications.

24 POWER TRANSMISSION AND DISTRIBUTION↗