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At least 181 records · Page 10

Portability for GPU-accelerated molecular docking applications for cloud and HPC: can portable compiler directives provide performance across all platforms?

High-throughput structure-based screening of drug-like molecules has become a common tool in biomedical research. Recently, acceleration with graphics processing units (GPUs) has provided a large performance boost for molecular docking programs. Both cloud and high-performance computing (HPC) resources have been used for large screens with molecular docking programs; while NVIDIA GPUs have dominated cloud and HPC resources, new vendors such as AMD and Intel are now entering the field, creating the problem of software portability across different GPUs. Ideally, software productivity could be maximized with portable programming models that are able to maintain high performance across architectures. While in many cases compiler directives have been used as an easy way to offload parallel regions of a CPU-based program to a GPU accelerator, they may also be an attractive programming model for providing portability across different GPU vendors, in which case the porting process may proceed in the reverse direction: from low-level, architecture-specific code to higher-level directive-based abstractions. MiniMDock is a new mini-application (miniapp) designed to capture the essential computational kernels found in molecular docking calculations, such as are used in phar-maceutical drug discovery efforts, in order to test different solutions for porting across GPU architectures. Here we extend MiniMDock to GPU offloading with OpenMP directives, and compare to performance of kernels using CUDA and HIP on NVIDIA and AMD GPUs, respectively, as well as across different compilers, exploring performance bottlenecks. We document this reverse-porting process, from highly optimized device code to a higher-level version using directives, compare code structure, and describe barriers that were overcome in this effort.

Thavappiragasam, Mathialakan↗

Scaling Laws of Graph Neural Networks for Atomistic Materials Modeling

Atomistic materials modeling is a critical task with wide-ranging applications, from drug discovery to materials science, where accurate predictions of the target material property can lead to significant advancements in scientific discovery. Graph Neural Networks (GNNs) represent the state-of-the-art approach for modeling atomistic material data thanks to their capacity to capture complex relational structures. While machine learning performance has historically improved with larger models and datasets, GNNs for atomistic materials modeling remain relatively small compared to large language models (LLMs), which leverage billions of parameters and terabyte-scale datasets to achieve remarkable performance in their respective domains. To address this gap, we explore the scaling limits of GNNs for atomistic materials modeling by developing a foundational model with billions of parameters, trained on extensive datasets in terabytescale. Our approach incorporates techniques from LLM libraries to efficiently manage large-scale data and models, enabling both effective training and deployment of these large-scale GNN models. This work addresses three fundamental questions in scaling GNNs: the potential for scaling GNN model architectures, the effect of dataset size on model accuracy, and the applicability of LLM-inspired techniques to GNN architectures. Specifically, the outcomes of this study include (1) insights into the scaling laws for GNNs, highlighting the relationship between model size, dataset volume, and accuracy, (2) a foundational GNN model optimized for atomistic materials modeling, and (3) a GNN codebase enhanced with advanced LLM-based training techniques. Our findings lay the groundwork for large-scale GNNs with billions of parameters and terabyte-scale datasets, establishing a scalable pathway for future advancements in atomistic materials modeling.

Li, Chaojian [ORNL] (ORCID:0000000340309777)↗

Optimizing FPGA-based Accelerator Design for Large-Scale Molecular Similarity Search (Special Session Paper)

Molecular similarity search has been widely used in drug discovery to rapidly identify structurally similar compounds from large molecular databases. With the increasing size of chemical libraries, there is growing interest in the efficient ac- celeration of large-scale similarity search. Existing works mainly focus on CPU and GPU to accelerate the computation of Tatimoto coefficient in measuring the pairwise similarity between different molecular fingerprints. In this paper, we propose and optimize an FPGA-based accelerator design on exhaustive and approximate search algorithms. On exhaustive search using BitBound & fold- ing, we analyze the similarity cutoff and folding level relationship with search speedup and accuracy, and propose a scalable on- the-fly query engine on FPGAs to reduce the resource utilization and pipeline interval. We achieve a 450 million compounds-per- second processing throughput for a single query engine. On approximate search using hierarchical navigable small world (HNSW), a popular algorithm with high recall and query speed, we propose an FPGA-based graph traversal engine to utilize high throughput register array based priority queue and fine- grained distance calculation engine to increase the processing capability. Experimental results show that the proposed FPGA- based HNSW implementation achieves a 35× speedup than existing works on CPU. To the best of our knowledge, our FPGA- based implementation is the first attempt to accelerate molecular similarity search on FPGA and has the highest performance among existing approaches.

Peng, Hongwu↗

Performance Portability of Molecular Docking Miniapp On Leadership Computing Platforms

Rapidly changing computer architectures, such as those found at high-performance computing (HPC) facilities, present the need for mini-applications (miniapps) that capture essential algorithms used in large applications to test program performance and portability, aiding transitions to new systems. The COVID-19 pandemic has fueled a flurry of activity in computational drug discovery, including the use of supercomputers and GPU acceleration for massive virtual screens for therapeutics. Recent work targeting COVID-19 at the Oak Ridge Leadership Computing Facility (OLCF) used the GPU-accelerated program AutoDock-GPU to screen billions of compounds on the Summit supercomputer. In this paper we present the development of a new miniapp, miniAutoDock-GPU, that can be used to evaluate the performance and portability of GPU-accelerated protein-ligand docking programs on different computer architectures. These tests are especially relevant as facilities transition from petascale systems and prepare for upcoming exascale systems that will use a variety of GPU vendors. The key calculations, namely, the Lamarckian genetic algorithm combined with a local search using a Solis-Wets based random optimization algorithm, are implemented. We developed versions of the miniapp using several different programming models for GPU acceleration, including a version using the CUDA runtime API for NVIDIA GPUs, and the Kokkos middle-ware API which is facilitated by C++ template libraries. A third version, currently in progress, uses the HIP programming model. These efforts will help facilitate the transition to exascale systems for this important emerging HPC application, as well as its use on a wide range of heterogeneous platforms.

Thavappiragasam, Mathialakan↗

Predicting Volume of Distribution in Humans: Performance of In Silico Methods for a Large Set of Structurally Diverse Clinical Compounds

Volume of distribution at steady state (V D,ss ) is one of the key pharmacokinetic parameters estimated during the drug discovery process. Despite considerable efforts to predict V D,ss , accuracy and choice of prediction methods remain a challenge, with evaluations constrained to a small set (<150) of compounds. To address these issues, a series of in silico methods for predicting human V D,ss directly from structure were evaluated using a large set of clinical compounds. Machine learning (ML) models were built to predict V D,ss directly and to predict input parameters required for mechanistic and empirical V D,ss predictions. In addition, log D, fraction unbound in plasma (fup), and blood-to-plasma partition ratio (BPR) were measured on 254 compounds to estimate the impact of measured data on predictive performance of mechanistic models. Furthermore, the impact of novel methodologies such as measuring partition (Kp) in adipocytes and myocytes (n = 189) on V D,ss predictions was also investigated. In predicting V D,ss directly from chemical structures, both mechanistic and empirical scaling using a combination of predicted rat and dog V D,ss demonstrated comparable performance (62%–71% within 3-fold). The direct ML model outperformed other in silico methods (75% within 3-fold, r 2 = 0.5, AAFE = 2.2) when built from a larger data set. Scaling to human from predicted V D,ss of either rat or dog yielded poor results (<47% within 3-fold). Measured fup and BPR improved performance of mechanistic V D,ss predictions significantly (81% within 3-fold, r 2 = 0.6, AAFE = 2.0). Adipocyte intracellular Kp showed good correlation to the V D,ss but was limited in estimating the compounds with low V D,ss .

59 BASIC BIOLOGICAL SCIENCES↗

Structural basis of a shared antibody response to SARS-CoV-2

Molecular understanding of neutralizing antibody responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) could accelerate vaccine design and drug discovery. We analyzed 294 anti–SARS-CoV-2 antibodies and found that immunoglobulin G heavy-chain variable region 3-53 (IGHV3-53) is the most frequently used IGHV gene for targeting the receptor-binding domain (RBD) of the spike protein. Co-crystal structures of two IGHV3-53–neutralizing antibodies with RBD, with or without Fab CR3022, at 2.33- to 3.20-angstrom resolution revealed that the germline-encoded residues dominate recognition of the angiotensin I converting enzyme 2 (ACE2)–binding site. This binding mode limits the IGHV3-53 antibodies to short complementarity-determining region H3 loops but accommodates light-chain diversity. These IGHV3-53 antibodies show minimal affinity maturation and high potency, which is promising for vaccine design. Knowledge of these structural motifs and binding mode should facilitate the design of antigens that elicit this type of neutralizing response.

59 BASIC BIOLOGICAL SCIENCES↗

Geometric deep learning of RNA structure

RNA molecules adopt three-dimensional structures that are critical to their function and of interest in drug discovery. Few RNA structures are known, however, and predicting them computationally has proven challenging. We introduce a machine learning approach that enables identification of accurate structural models without assumptions about their defining characteristics, despite being trained with only 18 known RNA structures. The resulting scoring function, the Atomic Rotationally Equivariant Scorer (ARES), substantially outperforms previous methods and consistently produces the best results in community-wide blind RNA structure prediction challenges. By learning effectively even from a small amount of data, our approach overcomes a major limitation of standard deep neural networks. Because it uses only atomic coordinates as inputs and incorporates no RNA-specific information, this approach is applicable to diverse problems in structural biology, chemistry, materials science, and beyond.

Townshend, Raphael J. L.↗

In silico trials predict that combination strategies for enhancing vesicular stomatitis oncolytic virus are determined by tumor aggressivity

Background Immunotherapies, driven by immune-mediated antitumorigenicity, offer the potential for significant improvements to the treatment of multiple cancer types. Identifying therapeutic strategies that bolster antitumor immunity while limiting immune suppression is critical to selecting treatment combinations and schedules that offer durable therapeutic benefits. Combination oncolytic virus (OV) therapy, wherein complementary OVs are administered in succession, offer such promise, yet their translation from preclinical studies to clinical implementation is a major challenge. Overcoming this obstacle requires answering fundamental questions about how to effectively design and tailor schedules to provide the most benefit to patients. Methods We developed a computational biology model of combined oncolytic vaccinia (an enhancer virus) and vesicular stomatitis virus (VSV) calibrated to and validated against multiple data sources. We then optimized protocols in a cohort of heterogeneous virtual individuals by leveraging this model and our previously established in silico clinical trial platform. Results Enhancer multiplicity was shown to have little to no impact on the average response to therapy. However, the duration of the VSV injection lag was found to be determinant for survival outcomes. Importantly, through treatment individualization, we found that optimal combination schedules are closely linked to tumor aggressivity. We predicted that patients with aggressively growing tumors required a single enhancer followed by a VSV injection 1 day later, whereas a small subset of patients with the slowest growing tumors needed multiple enhancers followed by a longer VSV delay of 15 days, suggesting that intrinsic tumor growth rates could inform the segregation of patients into clinical trials and ultimately determine patient survival. These results were validated in entirely new cohorts of virtual individuals with aggressive or non-aggressive subtypes. Conclusions Based on our results, improved therapeutic schedules for combinations with enhancer OVs can be studied and implemented. Our results further underline the impact of interdisciplinary approaches to preclinical planning and the importance of computational approaches to drug discovery and development.

60 APPLIED LIFE SCIENCES↗

Integrating and Characterizing HPC Task Runtime Systems for hybrid AI-HPC workloads

Scientific workflows increasingly involve both HPC and machine-learning tasks, combining MPI-based simulations, training, and inference in a single execution. Launchers such as Slurm’s srun constrain concurrency and throughput, making them unsuitable for dynamic and heterogeneous workloads. We present a performance study of RADICAL-Pilot (RP) integrated with Flux and Dragon, two complementary runtime systems that enable hierarchical resource management and high-throughput function execution. Using synthetic and production-scale workloads on Frontier, we characterize the task execution properties of RP across runtime configurations. RP+Flux sustains up to 930 tasks/s, and RP+Flux+Dragon exceeds 1,500 tasks/s with over 99.6% utilization. In contrast, srun peaks at 152 tasks/s and degrades with scale, with utilization below 50%. For IMPECCABLE.v2 drug discovery campaign, RP+Flux reduces makespan by 30–60% relative to srun/Slurm and increases throughput more than four times on up to 1,024. These results demonstrate hybrid runtime integration in RP as a scalable approach for hybrid AI-HPC workloads.

HPC-AI↗

Lustre Unveiled: Evolution, Design, Advancements, and Current Trends

The Lustre filesystem serves as a vital element in high-performance parallel storage, meeting the rising demands of scientific, research, and enterprise environments. Widely deployed across HPC environments, ranging from small-scale applications in AI/ML, to domains like oil and gas, drug discovery, and meteorology, and manufacturing, Lustre addresses the universal challenge of efficiently accessing vast and ever-increasing volumes of data. Lustre is the filesystem of choice on six out of the top 10 fastest supercomputers in the world today, over 65% of the top 100, and also for over 60% of the top 500. Despite its widespread popularity, there is a lack of a complete and up-to-date reference, covering Lustre’s evolution, design, and various advancements made over the years. In this journal, we aim to fill this gap by providing a comprehensive journey of Lustre, including its history with significant contributions to HPC, detailed architecture and design elements, exploration of advancements added through its evolution, and future directions. Additionally, we present a comparison of Lustre with other prominent storage technologies of the era. To illustrate the current state of Lustre, we analyze several filesystem trends, including utilization, performance, and usage patterns on Orion, the Lustre filesystem on the first exascale supercomputer Frontier. We hope that this journal serves as a comprehensive educational reference for the current and future generations interested in HPC filesystem storage aspects.

97 MATHEMATICS AND COMPUTING↗

Equivariant Graph Attention Network - 3D Conformers & Feature Fusion

EGAN-3F (Equivariant Graph Attention Network - 3D Conformers & Feature Fusion) presents an innovative approach for predicting binding affinity between small molecules and protein targets, a fundamental task in drug discovery. Traditional structure-based methods often depend on protein-ligand complex structures obtained from crystallography or molecular docking. In contrast, ligand-only machine learning models using 1D or 2D representations such as SMILES have been developed to predict binding affinity without structural information about the target; however, their accuracy is often limited due to the lack of 3D ligand information. EGAN-3F addresses this limitation by integrating spatially aware graph learning with traditional descriptor-based features. We systematically investigate how combining 2D and 3D molecular representations enhances binding affinity prediction from SMILES strings. This approach underscores the importance of modeling conformational diversity and incorporating chemically meaningful descriptors to improve predictive accuracy. The key innovation of EGAN-3F lies in its ability to achieve robust ligand-based binding affinity predictions without requiring protein-ligand complex structures, effectively bridging the gap between purely structural and ligand-only modeling paradigms.

Shim, Heesung [Lawrence Livermore National Laborat↗

Centrifugal Generation of Droplet-Based 3D Cell Cultures

Quickly and easily producing uniform populations of microsphere-based 3D cell cultures using droplet-based templating methods has the potential to enable widespread use of such platforms in drug discovery or cancer research. Here, we advance the design of centrifuge-based droplet generation devices, describe the use of this platform for droplet generation with controlled cell occupancy, and demonstrate weeklong culture duration. Using simple-to-construct devices and easily implemented protocols, the initial concentration of encapsulated cells is adjustable up to hundreds of cells per microsphere. This work demonstrates the first instance of using centrifugal droplet-generating devices to produce large numbers of cell-encapsulating microspheres. Applications of this versatile methodology include the rapid formation of templated 3D cell culture populations suitable for suspension culture or large batch bioreactor studies that require uniform populations.

Biochemistry & Molecular Biology↗

Chemical classification program synthesis using generative artificial intelligence

Accurately classifying chemical structures is essential for cheminformatics and bioinformatics, including tasks such as identifying bioactive compounds of interest, screening molecules for toxicity to humans, finding non-organic compounds with desirable material properties, or organizing large chemical libraries for drug discovery or environmental monitoring. However, manual classification is labor-intensive and difficult to scale to large chemical databases. Existing automated approaches either rely on manually constructed classification rules, or are deep learning methods that lack explainability. This work presents an approach that uses generative artificial intelligence to automatically write chemical classifier programs for classes in the Chemical Entities of Biological Interest (ChEBI) database. These programs can be used for efficient deterministic run-time classification of SMILES structures, with natural language explanations. The programs themselves constitute an explainable computable ontological model of chemical class nomenclature, which we call the ChEBI Chemical Class Program Ontology (C3PO). We validated our approach against the ChEBI database, and compared our results against deep learning models and a naive SMARTS pattern based classifier. C3PO outperforms the naive classifier, but does not reach the performance of state of the art deep learning methods. However, C3PO has a number of strengths that complement deep learning methods, including explainability and reduced data dependence. C3PO can be used alongside deep learning classifiers to provide an explanation of the classification, where both methods agree. The programs can be used as part of the ontology development process, and iteratively refined by expert human curators.

Artificial Intelligence↗

EvoDiffMol: evolutionary diffusion framework for 3D molecular design with optimized properties

Designing molecules with specific target properties remains a fundamental challenge in computational chemistry. While existing approaches show promise, most rely on simplified representations like SMILES strings or 2D graphs that lack essential three-dimensional geometric information. We present EvoDiffMol, a computational framework that integrates evolutionary algorithms with three-dimensional diffusion models for property-driven molecular generation. The method operates through adaptive evolutionary optimization, where population-based selection guides the generation process toward desired property landscapes. EvoDiffMol supports both unconstrained molecular design and scaffold-constrained generation that preserves fixed substructures while optimizing complementary regions. Comprehensive evaluation demonstrates exceptional performance, achieving the highest drug-likeness score (0.94) among all compared state-of-the-art methods while maintaining excellent validity, uniqueness, and novelty. Beyond single property optimization, the framework demonstrates flexible multi-property optimization capabilities, simultaneously controlling multiple molecular descriptors including synthetic accessibility, lipophilicity, topological polar surface area, and clinically relevant ADMET properties such as cardiotoxicity (hERG) and intestinal permeability (Caco-2). This adaptability spans from simple descriptors to practical pharmaceutical endpoints without requiring complete model retraining. The framework achieves precise control over target property values, generating molecules with properties closely matching specified targets for both single and multiple descriptors. Scaffold-constrained experiments preserve fixed molecular cores while maintaining effective property optimization. The three-dimensional representation offers advantages in maintaining structural validity during iterative optimization, with potential for geometry-aware applications in materials science and drug discovery.

3D molecular generation↗

Identification, characterization, and structure of a tRNA splicing enzyme RNA 5′-OH kinase from the pathogenic fungi Mucorales

Fungal Trl1 is an essential tRNA splicing enzyme composed of C-terminal cyclic phosphodiesterase and central polynucleotide kinase end-healing domains that convert the 2′,3′-cyclic-PO 4 and 5′-OH ends of tRNA exons into the 3′-OH,2′-PO 4 and 5′-PO 4 termini required for sealing by an N-terminal ATP-dependent ligase domain. Trifunctional Trl1 enzymes are present in most human fungal pathogens and are untapped targets for antifungal drug discovery. Mucorales species, deemed high-priority human pathogens by WHO, elaborate a noncanonical tRNA splicing apparatus in which a stand-alone monofunctional RNA ligase enzyme joins 3′-OH,2′-PO 4 and 5′-PO 4 termini. Here we identify a stand-aloneMucor circinelloidespolynucleotide kinase (MciKIN) and affirm its biological activity in tRNA splicing by genetic complementation in yeast. Recombinant MciKIN catalyzes magnesium-dependent phosphorylation of 5′-OH RNA and DNA ends in vitro. MciKIN displays a strong preference for GTP as the phosphate donor in the kinase reaction, a trait shared with the stand-alone RNA kinase homologs from Mucorales speciesRhizopus azygosporus(RazKIN) andLichtheimia corymbifera(LcoKIN) and with the kinase domains of fungal Trl1 enzymes. We report a 1.65 Å crystal structure of RazKIN in complex with GDP•Mg 2+ that illuminates the basis for guanosine nucleotide specificity.

Biochemistry & Molecular Biology↗

SARS-CoV2 Docking Dataset

Description: Small-molecule conformations and docking scores for 1.4 billion molecules docked against 6 protein targets from SARS-CoV2: MPro 5R84, MPro 6WQF, NSP15 6WLC, PLPro 7JIR, Spike 6M0J, and a hand-optimized model of the RNA-dependent RNA polymerase. Docking was carried out using the Autodock-GPU program performing 20 independent structure minimizations per dock - saving 3 results per molecule. Scores reported include the Autodock free energy estimate as well as RF3 and VS-DUD-E v2 machine-learned rescoring models. Protein structure files and maps in the format input to Autodock-GPU are included. Literature Ref: Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19, J. Chem. Inf. Model. 2020, 60(12): 5832–5852.

36 MATERIALS SCIENCE↗

National Virtual Biotechnology Laboratory: Report on Rapid R&D Solutions to the COVID-19 Crisis

With funding from the CARES Act, the U.S Department of Energy (DOE) established the National Virtual Biotechnology Laboratory (NVBL) in March 2020 to address key challenges associated with the COVID-19 crisis. NVBL brought together the broad scientific and technical expertise and resources of DOE’s 17 national laboratories to help tackle medical supply short ages, discover potential drugs to fight the virus, develop and validate COVID-19 testing methods, model disease spread and impact across the nation, and understand virus transport in buildings and the environment. National laboratory resources leveraged for this effort include a suite of world-leading user facilities broadly available to the research community, such as light and neutron sources, nanoscale science research centers, sequencing and biocharacterization facilities, and high-performance computing facilities. Within months, NVBL teams produced innovations in materials and advanced manufacturing that mitigated shortages in test kits and personal protective equipment (PPE), creating nearly 1,000 new jobs. They used DOE’s high-performance computers and light and neutron sources to identify promising candidates for antibodies and antivirals that universities and drug companies are now evaluating. NVBL researchers also developed new diagnostic targets and sample collection approaches, and supported U.S. Food and Drug Administration (FDA), Centers for Disease Control and Prevention (CDC), and U.S. Department of Defense (DoD) efforts to establish national guidelines used in administering millions of tests. Researchers used artificial intelligence and high-performance computing to produce near-real-time data analysis to forecast disease transmission, stress on public health infrastructure, and economic impact, which supported decision-makers at the local, state, and national levels. NVBL teams also studied how to control indoor virus movement to minimize uptake and protect human health. NVBL’s accomplishments demonstrate not only the powerful resource represented by DOE’s national laboratories working together to meet national needs, but also the effectiveness of the integrated NVBL framework for rapidly responding to emergencies with research and development (R&D) solutions. As the fight against COVID continues, sustained efforts are needed to confront this pandemic as well as future threats. Examples include: 1) Establishing “supply chains on demand” to meet emergency production needs by leveraging the materials and manufacturing expertise of DOE national laboratories and developing advances in electronics, sensing, robotics, and automation capabilities; 2) Improving the speed and robustness of drug discovery by integrating experimental platforms with DOE’s computational and experimental user facilities, which provide unique resources to support the discovery of high-potential therapeutic agents; 3) Protecting public, environmental, and animal health by developing new testing protocols and instrumentation adaptable to diverse sample types (both physiological and environmental) to quickly detect a wide range of pathogens and monitor other biorisks; 4) Supporting near-real-time data needs of decision-makers at the local, regional, state, and national levels by advancing data curation, analysis, and modeling using artificial intelligence and new data science tools for managing and evaluating large diverse datasets; 5) Harnessing DOE’s expertise in environmental modeling to design rooms and air handling for offices, classrooms, restaurants, and other structures to minimize biorisk transmissions. Going forward, NVBL is poised to apply the unique capabilities and expertise of the national laboratory complex to future national and international emergencies, both natural and engineered. Through this framework, the Office of Science will continue to be an integral component of agency wide efforts to prepare for and respond to biorisks and other crises.

42 ENGINEERING↗

Quantum Computing Market Report

The quantum computing market is entering a rapid growth phase. Growth was originally driven by private investment interest in high value applications such as drug discovery, materials science, and finance. Currently the main market drivers include technical advances, continued private investment, and rising public funding. The quantum computing market is poised for explosive growth — with its market size estimated at $1.42 billion USD in 2024, and an expected compound annual growth rate of 20.5% from 2025 to 2030 [4]. Superconducting qubits are the largest qubit type by revenue. However, alternative approaches such as trapped ion, neutral atom, spin based, and photonic qubits are also attracting investment.

97 MATHEMATICS AND COMPUTING↗