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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Artificial Intelligence and Machine Learning for Bioenergy Research: Opportunities and Challenges

The integration of artificial intelligence and machine learning (AI/ML) with automated experimentation, genomics, biosystems design, and bioprocessing technologies is poised to revolutionize scientific investigation and, particularly, bioenergy research. To identify the opportunities and challenges in this emerging research area, the U.S. Department of Energy’s (DOE) Biological and Environmental Research program (BER) and Bioenergy Technologies Office (BETO) held a joint virtual workshop on AI/ML for Bioenergy Research (AMBER) on August 23–25, 2022. These interests have since been amplified in a September 2022 Executive Order, “Advancing Biotechnology and Biomanufacturing Innovation for a Sustainable, Safe, and Secure U.S. Bioeconomy,” to promote a whole-of government approach to biotechnology development (White House 2022). Approximately 50 scientists with various backgrounds and expertise from academia, industry, and DOE national laboratories met to discuss the opportunities and challenges of AI/ML for bioenergy research. Workshop participants were tasked with assessing the potential for AI/ML and laboratory automation to advance biological understanding and engineering in general. They particularly examined how integrating AI/ML tools with laboratory automation could accelerate biosystems design and optimize biomanufacturing. Discussions included the data and computational infrastructure needed to augment biosystems design applications and the expertise and workforce development efforts urgently required to shift integrated systems toward bioenergy research more broadly. Participants discussed many existing and future applications of AI/ML for biosystems design ranging from enzymes to plants and microbes, microbiomes, and bioprocess development. They also identified three key categories of scientific and technical opportunities and challenges: high-quality data, AI/ML algorithms, and laboratory automation. Several main takeaways emerged from the workshop: 1. Numerous AI/ML and automated experimentation applications exist for a variety of DOE mission needs in energy and the environment; 2. Exemplary research grand challenges for which AI/ML could provide solutions include: building microbes and microbial communities to specifications, developing closed-loop autonomous design and control for biosystems design, and advancing scale-up and automation; 3. Lack of sufficient high-quality, annotated data hinders the development of AI/ML applications; 4. New and improved AI/ML tools are needed, particularly those meeting the specific needs of the BER and BETO research communities; 5. Trade-offs in performance, cost, and reliability exist between deploying commercially available versus building custom-developed instrumentation and software for automated or autonomous experimentation; translation of manual to automated or autonomous methods is often a nontrivial endeavor; 6. Training a new generation of young scientists who can develop and apply AI/ML tools is needed to solve long-standing scientific challenges in bioenergy research. The integration of AI/ML tools and automated experimentation represents a new data-driven research paradigm complementary to the traditional hypothesis-driven research paradigm. This paradigm accelerates design and optimization of biological systems and processes for a variety of DOE mission needs in energy and the environment. The AMBER workshop broadly explored the potential of this new paradigm for bioenergy research, of particular interest to BER and BETO, and identified key challenges and opportunities that DOE can address in the coming years by leveraging its unique capabilities and resources.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

A Blockchain and PKI-Based Secure Vehicle-to-Vehicle Energy-Trading Protocol

With the increasing awareness for sustainable future and green energy, the demand for electric vehicles (EVs) is growing rapidly, thus placing immense pressure on the energy grid. To alleviate this, local trading between EVs should be encouraged. In this paper, we propose a blockchain and public key infrastructure (PKI)-based secure vehicle-to-vehicle (V2V) energy-trading protocol. A permissioned blockchain utilizing the proof of authority (PoA) consensus and smart contracts is used to securely store data. Encrypted communication is ensured through transport layer security (TLS), with PKI managing the necessary digital certificates and keys. A multi-leader, multi-follower Stackelberg game-based trade algorithm is formulated to determine the optimal energy demands, supplies, and prices. Finally, we propose a detailed communication protocol that ties all the components together, enabling smooth interaction between them. Key findings, such as system behavior and performance, scalability of the trade algorithm and the blockchain, smart contract execution costs, etc., are presented through numerical results by implementing and simulating the protocol in various scenarios. This work not only enhances local energy trading among EVs, encouraging efficient energy usage and reducing burden on the power grid, but also paves a way for future research in sustainable energy management.

Stackelberg game↗
DOE OSTI2025

Clifford Circuit-Based Heuristic Optimization of Fermion-To-Qubit Mappings

Simulation of interacting Fermionic Hamiltonians is one of the most promising applications of quantum computers. However, the feasibility of analyzing Fermionic systems with a quantum computer hinges on the efficiency of Fermion-to-qubit mappings that encode nonlocal Fermionic degrees of freedom in local qubit degrees of freedom. While recent studies have highlighted the importance of designing Fermion-to-qubit mappings that are tailored to specific problem Hamiltonians, the methods proposed so far either are restricted to a narrow class of mappings or they use computationally expensive and unscalable brute-force search algorithms. Here, in this work, we address this challenge by designing a heuristic numerical optimization framework for Fermion-to-qubit mappings. To this end, we first translate the Fermion-to-qubit mapping problem to a Clifford circuit optimization problem and then use simulated annealing to optimize the average Pauli weight of the problem Hamiltonian. For all Fermionic Hamiltonians we have considered, the numerically optimized mappings outperform their conventional counterparts, including ternary-tree-based mappings that are known to be optimal for single creation and annihilation operators. We find that our optimized mappings yield between 15% and 40% improvements on the average Pauli weight when the simulation Hamiltonian has an intermediate level of complexity. Most remarkably, the optimized mappings improve the average Pauli weight for 6 × 6 nearest-neighbor hopping and Hubbard models by more than 40% and 20%, respectively. Surprisingly, we also find specific interaction Hamiltonians for which the optimized mapping outperforms any ternary-tree-based mapping. Our results establish heuristic numerical optimization as an effective method for obtaining mappings tailored for specific Fermionic Hamiltonian.

Hamiltonians↗
DOE OSTI2025

Desmearing small-angle scattering data by central moment expansions of instrument resolution

This study introduces an enhanced numerical technique tailored specifically for refining 1D small-angle scattering (SAS) intensity profiles affected by smearing. Our primary objective is to address the resolution blurring commonly encountered in SAS data, particularly in systems with clearly defined correlation peaks whose spread aligns with the width of the resolution function at corresponding Q positions. Unlike previous approaches that expanded the SAS intensity using central moment expansion, the new method focuses on expanding the resolution function itself, thus eliminating artificial oscillations observed in smeared spectra due to limitations inherent in our earlier algorithm. This method is straightforward to implement, computationally efficient and consistently performs well in numerical benchmarking. To illustrate its effectiveness, we present a case study of a lamellar phase characterized by distinct peaks in its small-angle neutron scattering intensities.

central moment expansions↗
DOE OSTI2023

Accurate real space iterative reconstruction (RESIRE) algorithm for tomography

Tomography has made a revolutionary impact on the physical, biological and medical sciences. The mathematical foundation of tomography is to reconstruct a three-dimensional (3D) object from a set of two-dimensional (2D) projections. As the number of projections that can be measured from a sample is usually limited by the tolerable radiation dose and/or the geometric constraint on the tilt range, a main challenge in tomography is to achieve the best possible 3D reconstruction from a limited number of projections with noise. Over the years, a number of tomographic reconstruction methods have been developed including direct inversion, real-space, and Fourier-based iterative algorithms. Here, we report the development of a real-space iterative reconstruction (RESIRE) algorithm for accurate tomographic reconstruction. RESIRE iterates between the update of a reconstructed 3D object and the measured projections using a forward and back projection step. The forward projection step is implemented by the Fourier slice theorem or the Radon transform, and the back projection step by a linear transformation. Our numerical and experimental results demonstrate that RESIRE performs more accurate 3D reconstructions than other existing tomographic algorithms, when there are a limited number of projections with noise. Furthermore, RESIRE can be used to reconstruct the 3D structure of extended objects as demonstrated by the determination of the 3D atomic structure of an amorphous Ta thin film. We expect that RESIRE can be widely employed in the tomography applications in different fields. Finally, to make the method accessible to the general user community, the MATLAB source code of RESIRE and all the simulated and experimental data are available at https://zenodo.org/record/7273314.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Noise Robustness and Experimental Demonstration of a Quantum Generative Adversarial Network for Continuous Distributions

Abstract The potential advantage of machine learning in quantum computers is a topic of intense discussion in the literature. Theoretical, numerical, and experimental explorations will most likely be required to understand its power. There have been different algorithms proposed to exploit the probabilistic nature of variational quantum circuits for generative modeling. In this paper, a hybrid architecture for quantum generative adversarial networks (QGANs) is employed and their robustness in the presence of noise is studied. A simple way of adding different types of noise to the quantum generator circuit is devised, and the noisy hybrid QGANs (HQGANs) are simulated numerically to learn continuous probability distributions, and to show that the performance of HQGANs remains unaffected. The effect of different parameters on the training time is also investigated to reduce the computational scaling of the algorithm and simplify its deployment on a quantum computer. The training on Rigetti's Aspen‐4‐2Q‐A quantum processing unit is then performed, and the results from the training are presented. The authors' results pave the way for experimental exploration of different quantum machine learning algorithms on noisy intermediate‐scale quantum devices.

Anand, Abhinav↗
DOE OSTI2024

Quantum Davidson algorithm for excited states

Abstract Excited state properties play a pivotal role in various chemical and physical phenomena, such as charge separation and light emission. However, the primary focus of most existing quantum algorithms has been the ground state, as seen in quantum phase estimation and the variational quantum eigensolver (VQE). Although VQE-type methods have been extended to explore excited states, these methods grapple with optimization challenges. In contrast, the quantum Krylov subspace (QKS) method has been introduced to address both ground and excited states, positioning itself as a cost-effective alternative to quantum phase estimation. However, conventional QKS methodologies depend on a pre-generated subspace through real or imaginary-time evolutions. This subspace is inherently expansive and can be plagued with issues like slow convergence or numerical instabilities, often leading to relatively deep circuits. Our research presents an economic QKS algorithm, which we term the quantum Davidson (QDavidson) algorithm. This innovation hinges on the iterative expansion of the Krylov subspace and the incorporation of a pre-conditioner within the Davidson framework. By using the residues of eigenstates to expand the Krylov subspace, we manage to formulate a compact subspace that aligns closely with the exact solutions. This iterative subspace expansion paves the way for a more rapid convergence in comparison to other QKS techniques, such as the quantum Lanczos. Using quantum simulators, we employ the novel QDavidson algorithm to delve into the excited state properties of various systems, spanning from the Heisenberg spin model to real molecules. Compared to the existing QKS methods, the QDavidson algorithm not only converges swiftly but also demands a significantly shallower circuit. This efficiency establishes the QDavidson method as a pragmatic tool for elucidating both ground and excited state properties on quantum computing platforms.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Quantum computing without quantum computers: Database search and data processing using classical wave superposition

Quantum computers are proven to be more efficient at solving a specific class of problems compared to traditional digital computers. Superposition of states and quantum entanglement are the two key ingredients that make quantum computing so powerful. However, not all quantum algorithms require quantum entanglement (e.g., search through an unsorted database). Is it possible to utilize classical wave superposition to speed up database searching as much as by using quantum computers? There were several attempts to mimic quantum computers using classical waves. It was concluded that the use of classical wave superposition comes with the cost of an exponential increase in resources. In this work, we consider the feasibility of building classical wave-based devices able to provide fundamental speedup over digital counterparts without the exponential overhead. We present experimental data on database searching through a magnetic database using spin wave superposition. The results demonstrate the same speedup as expected for quantum computers. Also, we present examples of numerical modeling demonstrating classical wave interference for period finding. This approach may not compete with quantum computers with efficiency but outperform classical digital computers. We argue that classical wave-based devices can perform some of the quantum algorithms with the same efficiency as quantum computers as long as quantum entanglement is not required.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

A Multifidelity Ensemble Kalman Filter with Reduced Order Control Variates

This work develops a new multi delity ensemble Kalman lter (MFEnKF) algorithm based on linear control variate framework. The approach allows for rigorous multi delity extensions of the EnKF, where the uncertainty in coarser delities in the hierarchy of models represent control variates for the uncertainty in ner delities. Small ensembles of high delity model runs are com- plemented by larger ensembles of cheaper, lower delity runs, to obtain much improved analyses at only small additional computational costs. We investigate the use of reduced order models as coarse delity control variates in the MFEnKF, and provide analyses to quantify the improvements over the traditional ensemble Kalman lters. We apply these ideas to perform data assimilation with a quasi-geostrophic test problem, using direct numerical simulation and a corresponding POD-Galerkin reduced order model. Numerical results show that the two- delity MFEnKF provides better analyses than existing EnKF algorithms at comparable or reduced computational costs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

MATBOX, an Open-Source Microstructure Analysis Toolbox for Meshing, Generation, Segmentation, and Characterization of 3D Heterogenous Volumes

Battery performance is strongly correlated with electrode microstructural properties. To account for its impact, lithium-ion battery (LIB) models either abstract the microstructural heterogeneity of composite electrodes using effective macroscopic properties (macro- or meso- scale models) or directly solve the system of equations on the microstructure geometry or mesh (microstructure-scale models). Therefore, to be adequate, both families of models require information from the microstructure geometry, which can be provided by the numerical tool presented in this work. MATBOX is a MATLAB open-source application [1] developed by NREL for performing various microstructure-related tasks including microstructure numerical generation, image filtering and microstructure segmentation, microstructure characterization and correlation, visualization, and microstructure meshing. MATBOX was originally developed for the analysis of LIB electrode microstructures; however, the algorithms provided by the toolbox are widely applicable to other heterogeneous materials. The toolbox provides a user-friendly experience thanks to a Graphical-User Interface, requires no coding by the user, and is well documented. This presentation will illustrate various MATBOX features for the characterization of a LIB electrode, including a fully automated Representative Volume Element (RVE) analysis, the numerical generation of complex 'virtual' microstructure, including dual-layer electrodes and carbon-binder additive phase, and the meshing of a complex NMC/graphite full cell microstructure suitable for 3D finite-element modeling. Other modules (segmentation, visualization, and correlation) will be briefly presented. Thanks to its modular, open-source approach, MATBOX can easily incorporate third-party algorithms to eventually build a standard in the field that will benefit the whole scientific community. Effective diffusion coefficient [2], additive phase numerical generation [3], and meshing [4] third-party algorithms have been already integrated in the toolbox with more to come.

DIRECT ENERGY CONVERSION,MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Cyber Physical Grid-Interactive Distributed Energy Resources Control for VPP Dispatch and Regulation: Preprint

This paper presents a cyber-physical algorithm for grid interactive DER control to enable two features of Virtual Power Plants (VPPs) dispatch and grid voltage regulation, considering the communication and security impacts. We first formulate the DER dispatch problem as a real-time, iterative, and grid-interactive DER control problem. Thereafter, we consider a probabilistic traffic model to characterize packet delays and loss in a communication network, and study how the delays enter the process of information exchange among the grid measurement units, local DER controllers and the grid control center that coordinately execute this dispatch algorithm. Finally, we propose a cyber-physical grid-interactive DER control algorithm using the previous message strategy. The tracking and regulation capabilities of this proposed algorithm can be made immune to the asynchrony resulting from the communications network traffic. We carry out simulations to show possible numerical instabilities and sensitivities of the tracking and regulation capabilities on the proposed strategy. Our results exhibit that the uncertainties of the underlying communications infrastructure must be considered in the control algorithm for the VPP tracking and regulation capabilities of any DER in a generic Cyber-Physical System (CPS).

co-simulation↗
DOE OSTI2022

An adaptive stochastic sequential quadratic programming with differentiable exact augmented lagrangians

In this study, we consider solving nonlinear optimization problems with a stochastic objective and deterministic equality constraints. We assume for the objective that its evaluation, gradient, and Hessian are inaccessible, while one can compute their stochastic estimates by, for example, subsampling. We propose a stochastic algorithm based on sequential quadratic programming (SQP) that uses a differentiable exact augmented Lagrangian as the merit function. To motivate our algorithm design, we first revisit and simplify an old SQP method Lucidi developed for solving deterministic problems, which serves as the skeleton of our stochastic algorithm. Based on the simplified deterministic algorithm, we then propose a non-adaptive SQP for dealing with stochastic objective, where the gradient and Hessian are replaced by stochastic estimates but the stepsizes are deterministic and prespecified. Finally, we incorporate a recent stochastic line search procedure Paquette and Scheinberg into the non-adaptive stochastic SQP to adaptively select the random stepsizes, which leads to an adaptive stochastic SQP. The global "almost sure" convergence for both non-adaptive and adaptive SQP methods is established. Numerical experiments on nonlinear problems in CUTEst test set demonstrate the superiority of the adaptive algorithm.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

An infeasible-start framework for convex quadratic optimization, with application to constraint-reduced interior-point and other methods

A framework is proposed for solving general convex quadratic programs (CQPs) from an infeasible starting point by invoking an existing feasible-start algorithm tailored for inequality-constrained CQPs. The central tool is an exact penalty function scheme equipped with a penalty-parameter updating rule. The feasible-start algorithm merely has to satisfy certain general requirements, and so is the updating rule. Under mild assumptions, the framework is proved to converge on CQPs with both inequality and equality constraints and, at a negligible additional cost per iteration, produces an infeasibility certificate, together with a feasible point for an (approximately) ℓ 1 -least relaxed feasible problem, when the given problem does not have a feasible solution. The framework is applied to a feasible-start constraint-reduced interior-point algorithm previously proved to be highly performant on problems with many more inequality constraints than variables (“imbalanced”). Numerical comparison with popular codes (OSQP, qpOASES, MOSEK) is reported on both randomly generated problems and support-vector machine classifier training problems. The results show that the former typically outperforms the latter on imbalanced problems. Finally, application of the proposed infeasible-start framework to other feasible-start algorithms is briefly considered, and is tested on a simplex iteration.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

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↗
DOE OSTI2022

Numerical gate synthesis for quantum heuristics on bosonic quantum processors

There is a recent surge of interest and insights regarding the interplay of quantum optimal control and variational quantum algorithms. We study the framework in the context of qudits which are, for instance, definable as controllable electromagnetic modes of a superconducting cavity system coupled to a transmon. By employing recent quantum optimal control approaches described in (Petersson and Garcia, 2021), we showcase control of single-qudit operations up to eight states, and two-qutrit operations, mapped respectively onto a single mode and two modes of the resonator. We discuss the results of numerical pulse engineering on the closed system for parametrized gates useful to implement Quantum Approximate Optimization Algorithm (QAOA) for qudits. The results show that high fidelity ( > 0.99) is achievable with sufficient computational effort for most cases under study, and extensions to multiple modes and open, noisy systems are possible. The tailored pulses can be stored and used as calibrated primitives for a future compiler in circuit quantum electrodynamics (cQED) systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

An algorithm for detecting and quantifying disturbance and recovery in high-frequency time series

Determining when a disturbance has occurred, its severity, and when the system recovered, is important to numerous questions in the aquatic sciences. This problem can be conceptualized as the timing and degree of perturbation from a typical state, and when the system returns to that typical state. We present an algorithm for detecting disturbance and recovery designed for high-frequency time series, e.g., data produced by automated sampling devices in instrumented buoys and flux towers. The algorithm quantifies differences in the empirical cumulative distribution functions of moving windows over reference and evaluation periods, and is sensitive to changes in the mean, variance, and higher statistical moments. Tests on simulated data show it accurately identifies disturbance and recovery. Three case studies illustrate the application of our algorithm in different empirical settings. A case study on dissolved oxygen in a Florida, USA estuary following a hurricane identified the disturbance and recovery 73 d later. A case study on air temperature and net ecosystem exchange in the Florida everglades identified cold snaps coinciding with periods of reduced carbon uptake. A case study on rotifer abundance following zebra mussel invasion in the Hudson River, NY showed rotifer collapse following invasion and recovery over a decade later. Methods such as ours can improve understanding response to disturbance and facilitate comparative and synthetic study of disturbance impacts across ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Adaptive sampling quasi-Newton methods for zeroth-order stochastic optimization

Here, we consider unconstrained stochastic optimization problems with no available gradient information. Such problems arise in settings from derivative-free simulation optimization to reinforcement learning. We propose an adaptive sampling quasi-Newton method where we estimate the gradients using finite differences of stochastic function evaluations within a common random number framework. We develop modified versions of a norm test and an inner product quasi-Newton test to control the sample sizes used in the stochastic approximations and provide global convergence results to the neighborhood of a locally optimal solution. We present numerical experiments on simulation optimization problems to illustrate the performance of the proposed algorithm. When compared with classical zeroth-order stochastic gradient methods, we observe that our strategies of adapting the sample sizes significantly improve performance in terms of the number of stochastic function evaluations required.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

An efficient high-order numerical solver for diffusion equations with strong anisotropy

In this paper, we present an interior penalty discontinuous Galerkin finite element scheme for solving diffusion problems with strong anisotropy arising in magnetized plasmas for fusion applications. Additionally, we demonstrate the accuracy produced by the high-order scheme and develop an efficient preconditioning technique to solve the corresponding linear system, which is robust to the mesh size and anisotropy of the problem. Several numerical tests are provided to validate the accuracy and efficiency of the proposed algorithm.

97 MATHEMATICS AND COMPUTING↗