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At least 1,567 records · Page 87
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DOE OSTI2021

Ab Initio Direct Dynamics

The reactivity and dynamics of molecular systems can be explored computationally by classical trajectory calculations. The traditional approach involves fitting a functional form of a potential energy surface (PES) to the energies from a large number of electronic structure calculations and then integrating numerous trajectories on this fitted PES to model the molecular dynamics. The ever-decreasing cost of computing and continuing advances in computational chemistry software have made it possible to use electronic structure calculations directly in molecular dynamics simulations without first having to construct a fitted PES. In this “on-the-fly” approach, every time the energy and its derivatives are needed for the integration of the equations of motion, they are obtained directly from quantum chemical calculations. This approach started to become practical in the mid-1990s as a result of increased availability of inexpensive computer resources and improved computational chemistry software. The application of direct dynamics calculations has grown rapidly over the last 25 years and would require a lengthy review article. The present Account is limited to some of our contributions to methods development and various applications. To improve the efficiency of direct dynamics calculations, we developed a Hessian-based predictor-corrector algorithm for integrating classical trajectories. Hessian updating made this even more efficient. Furthermore, this approach was also used to improve algorithms for following the steepest descent reaction paths. For larger molecular systems, we developed an extended Lagrangian approach in which the electronic structure is propagated along with the molecular structure. Strong field chemistry is a rapidly growing area, and to improve the accuracy of molecular dynamics in intense laser fields, we included the time-varying electric field in a novel predictor-corrector trajectory integration algorithm. Since intense laser fields can excite and ionize molecules, we extended our studies to include electron dynamics. Specifically, we developed code for time-dependent configuration interaction electron dynamics to simulate strong field ionization by intense laser pulses. Our initial application of ab initio direct dynamics in 1994 was to CH 2 O → H 2 + CO; the calculated vibrational distributions in the products were in very good agreement with experiment. In the intervening years, we have used direct dynamics to explore energy partitioning in various dissociation reactions, unimolecular dissociations yielding three fragments, reactions with branching after the transition state, nonstatistical dynamics of chemically activated molecules, dynamics of molecular fragmentation by intense infrared laser pulses, selective activation of specific dissociation channels by aligned intense infrared laser fields, angular dependence of strong field ionization, and simulation of sequential double ionization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Stochastic projective splitting

Here, we present a new, stochastic variant of the projective splitting (PS) family of algorithms for inclusion problems involving the sum of any finite number of maximal monotone operators. This new variant uses a stochastic oracle to evaluate one of the operators, which is assumed to be Lipschitz continuous, and (deterministic) resolvents to process the remaining operators. Our proposal is the first version of PS with such stochastic capabilities. We envision the primary application being machine learning (ML) problems, with the method’s stochastic features facilitating “mini-batch” sampling of datasets. Since it uses a monotone operator formulation, the method can handle not only Lipschitz-smooth loss minimization, but also min–max and noncooperative game formulations, with better convergence properties than the gradient descent-ascent methods commonly applied in such settings. The proposed method can handle any number of constraints and nonsmooth regularizers via projection and proximal operators. We prove almost-sure convergence of the iterates to a solution and a convergence rate result for the expected residual, and close with numerical experiments on a distributionally robust sparse logistic regression problem.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Peer-to-peer communication control for resilient operations of networked cyberphysical systems

This report includes two main accomplishments of the peer-to-peer communication control for resilient operation of networked microgrids project in FY24, which include a scheme for cyberattack-aware coordination of networked microgrids for supporting voltages of bulk power systems and a scheme for price signal-based operations of EV-rich networked microgrids with mixed ownership. First, the cyberattack-aware scheme enables networked microgrids to distributedly determine the amount of reactive power injection to support the voltage of bulk power system (BPS) in a fair manner. In this scheme, a risk-informed algorithm is presented to generate the peer-to- peer (P2P) communication graph with minimal risk of attack on communication links. To deal with cyberattacks on MG controllers, the resilient consensus algorithm (CA) is utilized for MG controllers to robustly estimate the total reactive power headroom, from which the MGs can accurately provide the needed amount of reactive power injection for supporting the voltage of BPS. The CA implementation and performance within the P2P communication framework are demonstrated on the IEEE 39-bus system with 6 microgrids contained in the distribution feeder under different cyberattack scenarios. Second, the price-based scheme enables the usage of the real-time price signal for the operations of electric vehicle (EV)-rich networked-microgrids with mixed ownership, in which not all the microgrids can communicate with the distribution system operator (DSO). In this scheme, a max consensus is introduced to enable the real-time price signal to be propagated from the DSO to all the microgrids, from which each microgrid controller will manage the DERs to balance the load demand and the power injection from the EV charging stations within its microgrid. Numerical results over one day with 288 slots of 5-minute intervals on the modified 123-node test feeder including 3 microgrids with high penetration of EV are presented to evaluate how the price signal affects the operations of networked microgrids under different charging strategies of the EV charging stations. The result indicates that our proposed EVCS (dis)charging strategy, which leverages the flexibility of EVs to support the grid through discharging during peak demand, proves to be a cost-effective solution that reduces operational costs while improving the social welfare of EV charging.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2026

Quantum-Inspired Bayesian Sampling for Uncertainty Quantification and Machine Learning (Final Technical Report)

With increasing simulation and measurement data, machine learning and artificial intelligence have been widely used in computational decision-making of complex engineering systems. The resulting tools, such as uncertainty quantification solvers, reinforcement learning, and physics-informed machine learning, have achieved great success in critical DOE tasks such as material discovery and design, energy system modeling and control, and numerical weather and climate prediction. A core topic in scientific machine learning and artificial intelligence is Bayesian inference: given an observed data set, people want to estimate the posterior distribution of a (possibly large) number of hidden parameters. Due to the flexibility and weak assumptions, Bayesian sampling has been the mainstream Bayesian inference solvers despite the rapid progress of approximate Bayesian inference. Classical Bayesian sampling methods such as Markov-chain Monte Carlo suffer from a low-acceptance rate due to the random walk nature, therefore state-of-the-art techniques use Hamiltonian Monte Carlo and its variants to efficiently draw posterior samples in a high dimension. The key idea of Hamiltonian Monte Carlo and its variants is to simulate the Hamiltonian dynamics of a classical particle with a fixed mass, and their performance significantly degrades when the posterior distribution is highly spiky or has multiple modes. Leveraging the idea of quantum physics, this project has investigated new theory, algorithms and applications of Bayesian inference (especially Bayesian sampling). The main results include: (1) novel quantum-inspired Bayesian sampling methods that can lead to better accuracy for challenging multi-modal or spiky distributions, (2) more scalable machine learning framework leveraging tensor-compressed Bayesian inference, and (3) Bayesian and sampling approaches for verifying the robustness of continuous and binary neural networks.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

A multifidelity Bayesian optimization method for inertial confinement fusion design

Due to their cost, experiments for inertial confinement fusion (ICF) heavily rely on numerical simulations to guide design. As simulation technology progresses, so too can the fidelity of models used to plan for new experiments. However, these high-fidelity models are by themselves insufficient for optimal experimental design, because their computational cost remains too high to efficiently and effectively explore the numerous parameters required to describe a typical experiment. Therefore, traditionally, ICF design has relied on low-fidelity modeling to initially identify potentially interesting design regions, which are then subsequently explored via selected high-fidelity modeling. In this paper, we demonstrate that this two-step approach can be insufficient: even for simple design problems, a two-step optimization strategy can lead high-fidelity searching toward incorrect regions and consequently waste computational resources on parameter regimes far away from the true optimal solution. We reveal that a primary cause of this behavior in ICF design problems is the presence of low-fidelity optima in different regions of the parameter space far away from high-fidelity optima. To address this issue, we propose an iterative multifidelity Bayesian optimization method based on Gaussian Process Regression that leverages both low- and high-fidelity models simultaneously. We demonstrate, using both two- and eight-dimensional ICF test problems, that our algorithm can effectively utilize both low-fidelity and high-fidelity models to refine the designs. This approach proves to be more efficient than relying solely on high-fidelity modeling for optimization.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Axion structure formation – II. The wrath of collapse

ABSTRACT The first paper in this series showed that quantum chromodynamic axion dark matter, as a highly correlated Bose fluid, contains extra-classical physics on cosmological scales. The source of the derived extra-classical physics is exchange–correlation interactions induced by the constraints of symmetric particle exchange and interaxion correlations from self-gravitation. The paper also showed that the impact of extra-classical physics on early structure formation is marginal, as the exchange–correlation interaction is inherently non-linear. This paper continues the study of axion structure formation into the non-linear regime, considering the case of full collapse and virialization. The N-body method is chosen to study the collapse, and its algorithms are derived for a condensed Bose fluid. Simulations of isolated gravitational collapse are performed for both Bose and cold dark matter fluids using a prototype N-body code. Unique Bose structures are found to survive even the most violent collapses. Bose post-collapse features include dynamical changes to global structures, creation of new broad sub-structures, violations of classical binding energy conditions, and new fine structures. Effective models of the novel structures are constructed and possibilities for their observation are discussed.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Efficient Multigrid Reduction-in-Time for Method-of-Lines Discretizations of Linear Advection

Parallel-in-time methods for partial differential equations (PDEs) have been the subject of intense development over recent decades, particularly for diffusion-dominated problems. It has been widely reported in the literature, however, that many of these methods perform quite poorly for advection-dominated problems. In this report we analyze the particular iterative parallel-in-time algorithm of multigrid reduction-in-time (MGRIT) for discretizations of constant-wave-speed linear advection problems. We focus on common method-of-lines discretizations that employ upwind finite differences in space and Runge-Kutta methods in time. Using a convergence framework we developed in previous work, we prove for a subclass of these discretizations that, if using the standard approach of rediscretizing the fine-grid problem on the coarse grid, robust MGRIT convergence with respect to CFL number and coarsening factor is not possible. This poor convergence and non-robustness is caused, at least in part, by an inadequate coarse-grid correction for smooth Fourier modes in space-time known as characteristic components. We propose an alternative coarse-grid operator that provides a better correction of these modes. This coarse-grid operator is related to previous work and uses a semi-Lagrangian discretization combined with an implicitly treated truncation error correction. Theory and numerical experiments show the proposed coarse-grid operator yields fast MGRIT convergence for many of the method-of-lines discretizations considered, including for both implicit and explicit discretizations of high order. Parallel results demonstrate speed-up over sequential time-stepping.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Theory for Equivariant Quantum Neural Networks

Quantum neural network architectures that have little to no inductive biases are known to face trainability and generalization issues. Inspired by a similar problem, recent breakthroughs in machine learning address this challenge by creating models encoding the symmetries of the learning task. This is materialized through the usage of equivariant neural networks the action of which commutes with that of the symmetry. In this work, we import these ideas to the quantum realm by presenting a comprehensive theoretical framework to design equivariant quantum neural networks (EQNNs) for essentially any relevant symmetry group. We develop multiple methods to construct equivariant layers for EQNNs and analyze their advantages and drawbacks. Our methods can find unitary or general equivariant quantum channels efficiently even when the symmetry group is exponentially large or continuous. As a special implementation, we show how standard quantum convolutional neural networks (QCNNs) can be generalized to group-equivariant QCNNs where both the convolution and pooling layers are equivariant to the symmetry group. We then numerically demonstrate the effectiveness of a S U ( 2 ) -equivariant QCNN over symmetry-agnostic QCNN on a classification task of phases of matter in the bond-alternating Heisenberg model. Our framework can be readily applied to virtually all areas of quantum machine learning. Lastly, we discuss about how symmetry-informed models such as EQNNs provide hopes to alleviate central challenges such as barren plateaus, poor local minima, and sample complexity. Published by the American Physical Society 2024

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Deep Learning for Automated Identification of Eels in Sonar Data

Freshwater eels, such as the American eel (Anguilla rostrata) present numerous challenges related to safe downstream fish passage at hydroelectric facilities. One of those challenges is effective monitoring of their abundance, movements, and behavior to facilitate design and operation of eel protection and passage facilities. A previous EPRI study documented the ability of human analysts to reliably identify American eels in data obtained with a 1100/1800 kHz, multibeam sonar. This report describes a project to develop deep learning (a subset of artificial intelligence) tools to automate the time-consuming, subjective process of eel identification in multibeam sonar data. The project exploited new data collected in the laboratory and the existing data from the prior EPRI field study to develop and test deep learning and other data analytic tools, including wavelet filtering, differencing for static object removal, and convolutional neural network analysis. The analysis of the laboratory data demonstrated feasibility of the approach, revealed object characteristics observed with the sonar that distinguish eels from similarly sized and shaped acoustic targets, and provided additional data for algorithm selection and training. Deep learning algorithms trained and tested on the laboratory data alone achieved accuracy rates of greater than 98% when classifying acoustic images of eels and similar-sized neutrally buoyant sticks. The algorithm trained and tested on the pre-existing field data alone, and yielded classification accuracy of 9.3% false positives and 13.3% false negatives when distinguishing between eels and sticks/PVC pipes based on video clips (i.e., multiple, consecutive images). This performance is comparable to the classification accuracy achieved by human analysts in the prior study. The deep learning algorithm trained on a combination of video clips obtained in the laboratory and the field and tested on video clips from the field, was able to distinguish eels from sticks and PVC pipes (a river debris analog) of similar size with 100% accuracy. Outreach to the hardware, software, and end-user communities early in the project helped to identify needs and specify the application space. Outreach to those communities at the end of the project communicated project results and opportunities for further development. The project achieved proof of concept for automated identification of eel in multibeam sonar data. Future work should focus on acquisition of additional data for more robust algorithm training and testing; modification of the software tools to accommodate multiple acoustic targets in the acoustic field at a given time; identification of additional object classes; incorporation of motion in the object identification and classification algorithms; operationalizing the software tools, including integration with other existing sonar data analysis tools; and partnering with hardware and software providers for distribution of the software tools with their commercial products.

13 HYDRO ENERGY↗
DOE OSTI2021

The HectoMAP Cluster Survey: Spectroscopically Identified Clusters and their Brightest Cluster Galaxies (BCGs)

We apply a friends-of-friends (FoF) algorithm to identify galaxy clusters and we use the catalog to explore the evolutionary synergy between brightest cluster galaxies (BCGs) and their host clusters. We base the cluster catalog on the dense HectoMAP redshift survey (2000 redshifts deg -2 ). The HectoMAP FoF catalog includes 346 clusters with 10 or more spectroscopic members within the range 0.05 < z < 0.55 and with a median z = 0.29. We list these clusters and their members. We also include central velocity dispersions (σ*, BCG ) for the FoF cluster BCGs, a distinctive feature of the HectoMAP FoF catalog. HectoMAP clusters with higher galaxy number density (80 systems) are all genuine clusters with a strong concentration and a prominent BCG in Subaru/Hyper Suprime-Cam images. The phase-space diagrams show the expected elongation along the line of sight. Lower-density systems include some low reliability systems. We establish a connection between BCGs and their host clusters by demonstrating that σ*, BCG /σ cl decreases as a function of cluster velocity dispersion (σ cl ), in contrast, numerical simulations predict a constant σ*, BCG /σ cl . Sets of clusters at two different redshifts show that BCG evolution in massive systems is slow over the redshift range z < 0.4. The data strongly suggest that minor mergers may play an important role in BCG evolution in clusters with σ cl ≳ 300 km s -1 . For lower mass systems (σ cl < 300 km s -1 ), major mergers may play a significant role. The coordinated evolution of BCGs and their host clusters provides an interesting test of simulations in high-density regions of the universe.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Local conservation of energy in fully implicit PIC algorithms

We consider the issue of strict, fully discrete local energy conservation for a whole class of fully implicit local-charge- and global-energy-conserving particle-in-cell (PIC) algorithms. Earlier studies demonstrated these algorithms feature strict global energy conservation. However, whether a local energy conservation theorem exists (in which the local energy update is governed by a flux balance equation at every mesh cell) for these schemes is unclear. In this study, we show that a local energy conservation theorem indeed exists. We begin our analysis with the 1D electrostatic PIC model without orbit-averaging, and then generalize our conclusions to account for orbit averaging, multiple dimensions, and electromagnetic models (Darwin). In all cases, a temporally, spatially, and particle-discrete local energy conservation theorem is shown to exist, proving that these formulations (as originally proposed in the literature), in addition to being locally charge conserving and globally energy conserving, are strictly locally energy conserving as well. In contrast to earlier proofs of local conservation in the literature, which only considered continuum time, our result is valid for the fully implicit time-discrete version of all models considered, including important features such as orbit averaging. We demonstrate the local-energy-conservation property numerically with a paradigmatic numerical example.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Emergence of a Spin Microemulsion in Spin-Orbit Coupled Bose-Einstein Condensates

We report the first numerical prediction of a “spin microemulsion”—a phase with undulating spin domains resembling classical bicontinuous oil-water-surfactant emulsions—in two-dimensional systems of spinor Bose-Einstein condensates with isotropic Rashba spin-orbit coupling. Using field-theoretic numerical simulations, we investigated the melting of a low-temperature stripe phase with supersolid character and find that the stripes lose their superfluidity at elevated temperature and undergo a Kosterlitz-Thouless-like transition into a spin microemulsion. Momentum distribution calculations highlight a thermally broadened occupation of the Rashba circle of low-energy states with macroscopic and isotropic occupation around the ring. Here, we provide a finite-temperature phase diagram that positions the emulsion as an intermediate, structured isotropic phase with residual quantum character before transitioning at higher temperature into a structureless normal fluid.

Finite temperature field theory↗
DOE OSTI2021

encore : an O ( N g2) estimator for galaxy N -point correlation functions

ABSTRACT We present a new algorithm for efficiently computing the N-point correlation functions (NPCFs) of a 3D density field for arbitrary N. This can be applied both to a discrete spectroscopic galaxy survey and a continuous field. By expanding the statistics in a separable basis of isotropic functions built from spherical harmonics, the NPCFs can be estimated by counting pairs of particles in space, leading to an algorithm with complexity $\mathcal {O}(N_\mathrm{g}^2)$ for Ng particles, or $\mathcal {O}(N_\mathrm{FFT}\log N_\mathrm{FFT})$ when using a Fast Fourier Transform with NFFT grid-points. In practice, the rate-limiting step for N > 3 will often be the summation of the histogrammed spherical harmonic coefficients, particularly if the number of radial and angular bins is large. In this case, the algorithm scales linearly with Ng. The approach is implemented in the encore code, which can compute the 3PCF, 4PCF, 5PCF, and 6PCF of a BOSS-like galaxy survey in ${\sim}100$ CPU-hours, including the corrections necessary for non-uniform survey geometries. We discuss the implementation in depth, along with its GPU acceleration, and provide practical demonstration on realistic galaxy catalogues. Our approach can be straightforwardly applied to current and future data sets to unlock the potential of constraining cosmology from the higher point functions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

A science-driven approach to optimize the design for a biological small-angle neutron scattering instrument

Biological small-angle neutron scattering (SANS) instruments facilitate critical analysis of the structure and dynamics of complex biological systems. However, with the growth of experimental demands and the advances in optical systems design, a new neutron optical concept is necessary to overcome the limitations of current instruments. This work presents an approach to include experimental objectives ( i.e. the science to be supported by a specific neutron scattering instrument) in the optimization of the neutron optical concept. The approach for a proposed SANS instrument at the Second Target Station of the Spallation Neutron Source at Oak Ridge National Laboratory, USA, is presented here. Further, the instrument is simulated with the McStas software package. The optimization process is driven by an evolutionary algorithm using McStas output data, which are processed to calculate an objective function designed to quantify the expected performance of the simulated neutron optical configuration for the intended purpose. Each McStas simulation covers the complete instrument, from source to detector, including realistic sample scattering functions. This approach effectively navigates a high-dimensional parameter space that is otherwise intractable; it allows the design of next-generation SANS instruments to address specific scientific cases and has the potential to increase instrument performance compared with traditional design approaches.

47 OTHER INSTRUMENTATION↗
DOE OSTI2026

End-To-End Decentralized Transmission Line Protection in IBR-Dominated Weak Grids Using Interpretable Data-Driven Methods

Traditional transmission line protection relies on predictable synchronous-based fault signatures, which frequently fail under the non-standard, current-limited fault characteristics of Inverter-Based Resources (IBRs). This study investigates how to achieve secure, communication-free fault isolation in IBR-dominated weak grids without relying on opaque, computationally heavy "black-box" machine learning algorithms. To address this, we propose a novel, standalone, and inherently interpretable data-driven protection framework. Unlike centralized methods requiring multi-terminal communication, this decentralized approach relies solely on local measurements using a hierarchical linear-kernel Support Vector Machine (SVM). The methodology decomposes the protection task into four sequential stages that mimic traditional protection elements: fault detection and fault direction identification, fault type classification, zone classification, and location estimation. This multi-stage architecture allows for specialized feature engineering at each stage, combining high computational efficiency with logic traceability. The framework's end-to-end performance was validated via C-code and PSCAD/EMTDC co-simulation, utilizing a real-world utility network and an OEM black-box IBR model. The proposed relay achieves 97.2% overall accuracy and provides a reliable trip decision within a 2.5-cycle window. The results confirm 100% accuracy in fundamental fault detection, reliable zone selectivity across low to moderate fault resistances, and robust security against non-fault transients, proving its immediate viability for integration into commercial numerical relays.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2022

Modeling electrokinetic flows with the discrete ion stochastic continuum overdamped solvent algorithm

In this article we develop an algorithm for the efficient simulation of electrolytes in the presence of physical boundaries. In previous work the discrete ion stochastic continuum overdamped solvent (DISCOS) algorithm was derived for triply periodic domains, and was validated through ion-ion pair correlation functions and Debye-Hückel-Onsager theory for conductivity, including the Wien effect for strong electric fields. In extending this approach to include an accurate treatment of physical boundaries we must address several important issues. First, the modifications to the spreading and interpolation operators necessary to incorporate interactions of the ions with the boundary are described. Next we discuss the modifications to the electrostatic solver to handle the influence of charges near either a fixed potential or dielectric boundary. An additional short-ranged potential is also introduced to represent interaction of the ions with a solid wall. Finally, the dry diffusion term is modified to account for the reduced mobility of ions near a boundary, which introduces an additional stochastic drift correction. Herein, several validation tests are presented confirming the correct equilibrium distribution of ions in a channel. Additionally, the methodology is demonstrated using electro-osmosis and induced-charge electro-osmosis, with comparison made to theory and other numerical methods. Notably, the DISCOS approach achieves greater accuracy than a continuum electrostatic simulation method. We also examine the effect of under-resolving hydrodynamic effects using a “dry diffusion” approach, and find that considerable computational speedup can be achieved with a negligible impact on accuracy.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

A hybrid finite volume method and smoothed particle hydrodynamics approach for efficient and accurate blast simulations

Modeling strong shock waves in fluids remains a persistent challenge in computational physics. Essential to research efforts in industry and defense, numerous methods have been devised to improve the accuracy and efficiency of shock simulations. A novel, hybrid Finite Volume Method (FVM)-Smoothed Particle Hydrodynamics (SPH) approach is capable of further improving efficiency and retaining accuracy by exploiting the favorable characteristics of each respective method. This hybrid approach is presented for shock capturing in compressible fluids. The Python framework Pyro2 is employed to simulate a coarse FVM mesh, while the Python framework PySPH is utilized to model the fluid in regions with high gradients through SPH particles. The performance of the hybrid FVM-SPH scheme, compared to the individual FVM and SPH methods, is assessed in 1 kt and 10 kt blast simulations. Our results indicate that the hybrid approach offers higher computational efficiency than SPH while preserving its accuracy and characteristics. The hybrid approach had a relative speedup of 11.3x and 22.3x over the FVM and SPH approaches for the 1 kt simulation and a relative speedup of 14.7x and 20.9x over the FVM and SPH approaches for the 10 kt simulation. The hybrid SPH algorithm enables future compressible fluid simulations with more extensive capabilities than grid-based methods alone, presenting potential applications in modeling fluid-structure interactions and solid deformation and fracturing in blast simulations.

Myers, Conner↗
DOE OSTI2025

Assessing the potential of deep learning for protein–ligand docking

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein–ligand docking have recently been introduced, so far no previous works have systematically studied the behaviour of the latest docking and structure prediction methods within the broadly applicable context of: (1) using predicted (apo) protein structures for docking (for example, for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (for example, for enzyme design); and (3) having no previous knowledge of binding pockets (for example, for generalization to unknown pockets). To enable a deeper understanding of the real-world utility of docking methods, we introduce PoseBench, a comprehensive benchmark for broadly applicable protein–ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein–ligand docking and protein–ligand structure prediction using both primary ligand and multiligand benchmark datasets, the latter of which we introduce to the DL community. Empirically, using PoseBench, we find that: (1) DL cofolding methods generally outperform comparable conventional and DL docking baseline algorithms, but popular methods such as AlphaFold 3 are still challenged by prediction targets with new protein–ligand binding poses; (2) certain DL cofolding methods are highly sensitive to their input multiple sequence alignments, whereas others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting new or multiligand protein targets.

Morehead, Alex [Lawrence Berkeley National Laborat↗