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NASA NTRS2011

Ndarts

Ndarts software provides algorithms for computing quantities associated with the dynamics of articulated, rigid-link, multibody systems. It is designed as a general-purpose dynamics library that can be used for the modeling of robotic platforms, space vehicles, molecular dynamics, and other such applications. The architecture and algorithms in Ndarts are based on the Spatial Operator Algebra (SOA) theory for computational multibody and robot dynamics developed at JPL. It uses minimal, internal coordinate models. The algorithms are low-order, recursive scatter/ gather algorithms. In comparison with the earlier Darts++ software, this version has a more general and cleaner design needed to support a larger class of computational dynamics needs. It includes a frames infrastructure, allows algorithms to operate on subgraphs of the system, and implements lazy and deferred computation for better efficiency. Dynamics modeling modules such as Ndarts are core building blocks of control and simulation software for space, robotic, mechanism, bio-molecular, and material systems modeling.

Jain, Abhinandan↗

NASA NTRSDate not supplied

Computationally Guided Design of Polymer-Coated Microparticles as Reusable Materials

Long-duration space exploration missions and sustained lunar or Martian surface operations present greater demands for multifunctional and reusable materials. By scaling down the amount of material to be launched from Earth, both mission cost and risk can be reduced. In this regard, leveraging in-space manufacturing capabilities with reusable feedstock materials is an attractive option, as it will allow for articles to be generated on demand, utilized, and then recycled for additional use. NASA’s Enabling Sustained Presence Using Recyclables (ESPUR) project aims to develop reusable materials using polymer-coated microparticles that are bonded via reversible Diels-Alder reactions, where only modest heat is needed to trigger the reverse reaction and enable reuse. For proof-of-concept demonstration, research is currently focused on the fabrication of epoxy microparticles that contain a copoly(carbonate urethane) coating with maleimide and furan functionalities. Here, we discuss the integration of computational materials modeling approaches to help navigate the large design space in this development effort. We perform molecular dynamics (MD) simulations with atomistic and coarse-grained models of the copolymer, which allow us to evaluate the effects of design parameters like the molecular weight and composition on the molecular interactions and chain dynamics. We show how the properties change with the reversible bonds. We also leverage discrete element method (DEM) simulations to assess how microparticle design parameters like the size ratio and volume fraction can be tuned to increase the packing density and number of microparticle contacts to improve the mechanical properties. Our results demonstrate how computational tools can be used in close collaboration with experimental efforts to accelerate material design.

reusable materials↗

DOE OSTI2022

Sequence-defined Pareto frontier of a copolymer structure

The correlations between the sequence of monomers in a macromolecule and its three-dimensional (3D) structure is a grand challenge in polymer science. The properties and functions of macromolecules depend on their 3D shape that has appeared to be dictated by their monomer sequence. However, the progress towards understanding the sequence–structure-property correlations and their utilization in materials engineering are slow because it is almost impossible to characterize an astronomically large number of possible sequences of a copolymer using traditional experimental and simulation methods. To address this problem, here, we combine evolutionary computing and coarse-grained molecular dynamics (CGMD) simulation and study the sequence-structure correlations of a model AB-type copolymer in a solution and assess the impact of sequence on the packing density in its bulk phase. The CGMD-based evolutionary algorithm (EA) screens the sequence space of a single chain copolymer efficiently and identifies a wide range of single-molecule structures including extremal radii of gyration. The data are utilized to estimate the Pareto front of the structure-space of a binary copolymer as a function of its composition. The monomer packings in single-molecule solution phase and multimolecular bulk phase are found to be identical. Finally, this work highlights the opportunities of sequence-specific control of macromolecular structure for designing target materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Analytic Nuclear Gradients Including Oriented External Electric Fields in a Molecule-Fixed Frame

Electric-field-assisted chemistry has attracted much attention in recent years, particularly in the context of oriented external electric fields for controlling molecular structure and reactivity. Such fields have been explored in a wide range of applications, including switching materials, nanoparticles, controllable catalysts, medicines, and clinical therapies. However, the determination of fixed fields in the laboratory frame becomes ineffective for flexible molecules, as conformational changes can significantly alter the relative orientation between the applied field and molecular structure. In this work, we propose two molecular reference frames─the principal axis frame and the local reference frame─to define oriented electric fields within the molecular framework. These coordinate systems powerfully eliminate ambiguities in the relative orientation between the applied field and the molecule. Analytic nuclear gradients in the presence of external electric fields are derived and implemented, with an initial application to field-dependent geometry optimizations of cis - and trans -formanilide. Analysis of the resulting field-induced equilibrium structures reveals distinct structural responses, validating the accuracy and robustness of the proposed formalism. The analytic gradient framework enables systematic investigations of molecular properties and reactivity under arbitrarily oriented electric fields, opening new opportunities for computational modeling and rational design in electric-field-controlled chemistry.

electric fields↗

DOE OSTI2023

Multifunctional Chiral Chemically‐Powered Micropropellers for Cargo Transport and Manipulation

Practical applications of synthetic self-propelled nano and microparticles for microrobotics, targeted drug delivery, and manipulation at the nanoscale are rapidly expanding. However, fabrication limitations often hinder progress, resulting in relatively simple shapes and limited functionality. Here, taking advantage of 3D nanoscale printing, chiral micropropellers powered by the hydrogen peroxide reduction reaction are fabricated. Due to their chirality, the propellers exhibit multifunctional behavior controlled by an applied magnetic field: spinning in place (loitering), directed migration in the prescribed direction, capture, and transport of polymer cargo particles. Design parameters of the propellers are optimized by computation modeling based on mesoscale molecular dynamics. It is predicted by computer simulations, and confirmed experimentally, that clockwise rotating propellers attract each other and counterclockwise repel. These results shed light on how chirality and shape optimization enhance the functionality of synthetic autonomous micromachines.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Neural Phase Simulation

The Neural Phase Simulation (NPS) is a package of codes for simulating microstructure evolution and accelerated molecular dynamics with deep neural-networks based surrogate models. NPS is designed to offer quantitatively accurate and computationally efficient simulation capabilities by leveraging modern machine-learning techniques. The primary intended use cases of NPS are training neural network surrogate models, though performing simulations on a single node is also supported. The NPS surrogate models can be trained from ground truth simulation methods, which are supposed to be accurate but expensive, such as molecular dynamics, phase field methods, kinetic Monte Carlo and discrete dislocation dynamics.

Zhou, Fei↗

DOE OSTI2022

Universal Solvent Viscosity Reduction via Hydrogen Bonding Disruptors

Liquid Ion Solutions LLC (DBA RoCo Global) in partnership with Carnegie Mellon University and Carbon Capture Scientific LLC, has performed lab-scale development and evaluation of novel additives that lower the viscosity of water-lean amine solvents for post-combustion carbon dioxide capture. This project focuses on developing additives that minimize the formation of long-range electrostatic and hydrogen bonding (HB) networks, decreasing the solvent viscosity, improving diffusion, and improving the process economics. The project objectives included: 1) performing computer simulation to understand the molecular interactions of the additive molecules in water-lean CO 2 capture solvents, 2) design and synthesis of HB disruptors additives, 3) performance testing with additive molecules on model amine solvents, and 4) demonstration of the effectiveness of the optimized additives in the presence of synthetic flue gas. To meet the abovementioned objectives, the project team utilized a holistic approach that combines molecular simulation, experimental testing, and economic analysis studies. The project team developed ab initio molecular model and then perform computer simulation to develop relationship between hydrogen bonding, viscosity, and performed quantitative analysis of additive on the viscosity of the solvent. The team completed computational comparative study on a range of organic functional groups such as ethers, esters, cyclic carbonates, alkanes, and ammonium salts for their effect on viscosity gaining key insights into molecular interactions and the impact of various functional groups and molecular shapes on viscosity. Assisted with molecular simulation insights, the project team conducted additive synthesis and testing, including a proof-of-concept study, additive screening, optimization, and synthetic flue gas testing. The experimental proof-of-concept study proved that the hydrogen bonding acceptors result in significant decrease of viscosities. Detailed additive screening (exploring various functionalities and molecular structures) has been performed. Several promising additives showed excellent reduction in viscosity (30-41%) at 5% additive loading, and over 50% viscosity reduction at 10% additive loading for the model solvents. The team also performed complex screening studies on additive loadings and mixing effect among additives using the design of experiments. Based on multiple screening experiments, one additive-solvent candidate was down-selected for synthetic flue gas testing. A 100-hour continuous absorption/desorption study was conducted under simulated flue gas using a lab-scale continuous capture and separation system. No degradation (for both solvent and additive) was observed based on the GC results of the solvent samples collected from the continuous study. The team conducted preliminary engineering analyses and cost-benefit analyses to quantify the potential economic benefits of the additive approach for solvent viscosity reduction. Based on the experimental data, CO 2 capture cost savings from the capital and operating cost savings are estimated at $\$$4.7/tonne and $\$$0.3/tonne CO 2 captured, respectively. Considering the additive cost, the net benefit is estimated to be between $\$$4.32~$\$$4.86/tonne CO 2 captured.

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2025

The design space of E(3)-equivariant atom-centred interatomic potentials

Abstract Molecular dynamics simulation is an important tool in computational materials science and chemistry, and in the past decade it has been revolutionized by machine learning. This rapid progress in machine learning interatomic potentials has produced a number of new architectures in just the past few years. Particularly notable among these are the atomic cluster expansion, which unified many of the earlier ideas around atom-density-based descriptors, and Neural Equivariant Interatomic Potentials (NequIP), a message-passing neural network with equivariant features that exhibited state-of-the-art accuracy at the time. Here we construct a mathematical framework that unifies these models: atomic cluster expansion is extended and recast as one layer of a multi-layer architecture, while the linearized version of NequIP is understood as a particular sparsification of a much larger polynomial model. Our framework also provides a practical tool for systematically probing different choices in this unified design space. An ablation study of NequIP, via a set of experiments looking at in- and out-of-domain accuracy and smooth extrapolation very far from the training data, sheds some light on which design choices are critical to achieving high accuracy. A much-simplified version of NequIP, which we call BOTnet (for body-ordered tensor network), has an interpretable architecture and maintains its accuracy on benchmark datasets.

Computer Science↗

NASA NTRS2000

Overview of Nanobiotechnology

The ability to manipulate matter at the atomic and molecular levels is likely to change the way almost everything is designed and made, from computers to engineering systems to objects not yet imagined. For nanometer-scale objects, biological systems provide a rich storehouse of interesting ideas and strategies, and this is why there has been synergistic coupling between nanotechnology and biotechnology. The field of nanobiotechnology is garnering much interest around the world. In January 2000, the President announced the establishment of the National Nanotechnology Initiative and has made it a top priority. An attempt is made in this overview to define some of the buzzwords and set the stage for the succeeding presentations. This presentation is divided into four parts. The first part identifies the major characteristics of future aerospace systems that distinguish them from the current systems. The second and third parts describe the revolutionary and key technologies and future research and learning environments required for the realization of future systems. The fourth part lists the objectives of the workshop and the sources of information about nano and biotechnologies. This document consists of viewgraphs with an explanation for each slide.

Ahmed K. Noor↗

DOE OSTI2024

A generative artificial intelligence framework based on a molecular diffusion model for the design of metal-organic frameworks for carbon capture

Metal-organic frameworks (MOFs) exhibit great promise for CO 2 capture. However, finding the best performing materials poses computational and experimental grand challenges in view of the vast chemical space of potential building blocks. Here, we introduce GHP-MOFassemble, a generative artificial intelligence (AI), high performance framework for the rational and accelerated design of MOFs with high CO 2 adsorption capacity and synthesizable linkers. GHP-MOFassemble generates novel linkers, assembled with one of three pre-selected metal nodes (Cu paddlewheel, Zn paddlewheel, Zn tetramer) into MOFs in a primitive cubic topology. GHP-MOFassemble screens and validates AI-generated MOFs for uniqueness, synthesizability, structural validity, uses molecular dynamics simulations to study their stability and chemical consistency, and crystal graph neural networks and Grand Canonical Monte Carlo simulations to quantify their CO 2 adsorption capacities. We present the top six AI-generated MOFs with CO 2 capacities greater than 2m mol g -1 , i.e., higher than 96.9% of structures in the hypothetical MOF dataset.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1980

Shuttle/Payload Contamination Evaluation /SPACE/ - A systems level contamination model

The Shuttle/Payload Contamination Evaluation (SPACE) computer program was designed to three dimensionally synthesize the dynamics of the induced on-orbit molecular contaminant environment of the Shuttle Orbiter and a number of Spacelab payload carrier configurations. SPACE has the capability to accept any instrument or spacecraft configuration for contamination evaluation through manipulation of program input data. It represents a significant advancement over previous analytical or modeling techniques in that it is the first integrated systems level model of its type to collectively consider geometry (emphasizing surface shadowing), any arbitrary contaminant source(s) and the contaminant transport mechanisms of: (1) direct source-to-surface; (2) return flux due to molecular collisions with the ambient atmosphere and other contaminant molecules; and (3) reflection/reemission from structural surfaces.

Jarossy, F. J.↗

NASA NTRS2018

Aladyn - Adaptive Neural Network Molecular Dynamics Simulation Code: Computational Materials Mini-Application

This report provides an overview and commands description of the Computational Materials mini-application, Aladyn. Aladyn is a simple molecular dynamics code written in FORTRAN 2008, which is designed to demonstrate the use of adaptive neural networks (ANNs) in atomistic simulations. The role of ANNs is to reproduce the very complex energy landscape resulting from the atomic interactions in materials with the accuracy of quantum mechanics-based energy calculations. The ANN is trained on a large set of atomic structures calculated using the density functional theory (DFT) method. The Aladyn code is being released to serve as a training testbed for students and professors in academia to explore possible optimization algorithms for parallel computing on multicore central processing unit (CPU) computers or computers utilizing many core architectures based on graphic processing units (GPUs). The effort is related to the High Performance Computing Incubator (HPCI) project at NASA Langley Research Center.

Yamakov, Vesselin I.↗

DOE OSTI2025

Reticular Materials and AI-Driven Computer Simulations for Seawater Mining of Valuable Metals (Final Technical Report)

This Final Technical Report describes our exploratory efforts that combine reticular materials synthesis (hydrolytically robust metal–organic frameworks, MOFs) with AI‑enabled molecular simulations to develop mechanistic, quantitative design rules for recovering lithium and other alkali-metal ions from highly dilute, competitive aqueous resources (e.g., seawater). The central outcome is a joint experimental–computational study of ion uptake in MOF‑808 (Chemical Science, 2025) that quantifies both thermodynamics and kinetics of Li + , Na + , and K + uptake and identifies how pore size, pore hydration state, dehydration penalties, and pore-window transport barriers govern selectivity. Guided by these insights, we synthesized and tested functionalized MOF‑808 and multivariate MOFs incorporating ion-recognition motifs (including carboxylates and crown-ether linkers) and evaluated uptake in synthetic seawater, highlighting framework topology and pore chemistry as levers for improved Li + /Na + discrimination. We also developed transferable simulation models, enhanced-sampling protocols, and automated workflows that enable systematic screening of porous sorbents.

42 ENGINEERING↗

DOE OSTI2026

Identification of Solid-Electrolyte Interphase Species by Joint Characterization of Li-Ion Battery Chemistry by Mass Spectrometry and Electrochemical Reaction Networks

The formation and stability of the solid-electrolyte interphase (SEI) play central roles in determining the long-term performance and safety of modern electrochemical energy storage systems. Despite decades of research, the SEI’s heterogeneous, dynamic, and multiphase nature has defied comprehensive molecular-level characterization, creating a critical knowledge gap that limits rational battery design. In this work, we introduce a computational−experimental framework that integrates high-throughput quantum chemistry calculations, data-driven electrochemical reaction networks (eCRNs), stochastic algorithms, and laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (LDI-FTICR-MS) to unravel SEI formation in carbonatebased electrolytes without imposing predefined mechanisms. We constructed the most comprehensive eCRN to date, spanning over 10,000 species and 209 million reactions. Through stochastic network analysis, we successfully recovered 27 species that were previously reported in the literature and predicted 28 novel SEI species nearly doubling our scientific knowledge in this area. Each new species was rigorously confirmed through advanced mass spectral analysis of its distinct molecular and isotopic signatures. We kinetically refined the formation pathways for a select set of both previously reported and novel SEI products, revealing kinetically feasible elementary reaction mechanisms with activation barriers below 1 eV. This computational−experimental approach deepens our molecular-level understanding of SEI chemistry by resolving which species form and through which decomposition mechanisms they emerge. Such knowledge provides the foundation necessary to connect electrolyte composition to the resulting SEI components, a critical step toward a more informed electrolyte development in next-generation lithium-based batteries.

25 ENERGY STORAGE↗

DOE OSTI2022

De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV -2 spike receptor binding domain ( RBD )

The continued emergence of new SARS-CoV-2 variants has accentuated the growing need for fast and reliable methods for the design of potentially neutralizing antibodies (Abs) to counter immune evasion by the virus. Here, we report on the de novo computational design of high-affinity Ab variable regions (Fv) through the recombination of VDJ genes targeting the most solvent-exposed hACE2-binding residues of the SARS-CoV-2 spike receptor binding domain (RBD) protein using the software tool OptMAVEn-2.0. Subsequently, we carried out computational affinity maturation of the designed variable regions through amino acid substitutions for improved binding with the target epitope. Immunogenicity of designs was restricted by preferring designs that match sequences from a 9-mer library of “human Abs” based on a human string content score. We generated 106 different antibody designs and reported in detail on the top five that trade-off the greatest computational binding affinity for the RBD with human string content scores. We further describe computational evaluation of the top five designs produced by OptMAVEn-2.0 using a Rosetta-based approach. We used Rosetta SnugDock for local docking of the designs to evaluate their potential to bind the spike RBD and performed “forward folding” with DeepAb to assess their potential to fold into the designed structures. Ultimately, our results identified one designed Ab variable region, P1.D1, as a particularly promising candidate for experimental testing. This effort puts forth a computational workflow for the de novo design and evaluation of Abs that can quickly be adapted to target spike epitopes of emerging SARS-CoV-2 variants or other antigenic targets.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

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↗

DOE OSTI2023

Engineering Supramolecular Hybrid Architectures with Directional Organofluorine Bonds

Understanding how chemical modifications alter the atomic‐scale organization of materials is of fundamental importance in materials engineering and the target of considerable efforts in computational prediction. Incorporating covalent and noncovalent interactions in designing crystals while “piggybacking” on the driving force of molecular self‐assembly has augmented efforts to understand the emergence of complex structures using directed synthesis. In this work, microcrystalline powders of the silver 2‐, 3‐, and 4‐fluorobenzenethiolates are prepared and their structures are resolved by small‐molecule serial femtosecond X‐ray crystallography. These three compounds enable the emergence and role of supramolecular synthons in the crystal structures of 3D metal‐organic chalcogenolates to be examined. The unique divergence in their optoelectronic, morphological, and structural behaviors is assessed. The extent of CHF interactions and their influence on the structure and the observed trends in the thermal stability of the crystals are quantified through theoretical calculations and thermogravimetric analysis.

Kotei, Patience A.↗

DOE OSTI2024

Computational Exploration of High Entropy Alloys as Promising Materials for Future Beam Windows

With the ever-increasing demand for high beam power, the currently used beam-intercepting devices (BIDs) such as targets, and beam windows may not be able to handle the high power required for future accelerator complexes or the lifetime may be reduced drastically. As beam power increases, the damage incurred by BIDs, including thermal shock, fatigue, and irradiation damage, also rises. Therefore, it is imperative to design materials that can withstand high beam power for longer lifetimes. High entropy alloys (HEAs) have emerged as potential alternative materials for designing next-generation BIDs. In this study, we primarily focus on materials for developing beam windows for next-generation accelerator complexes. We propose an integrated approach that combines various computational techniques to study and design new materials. Specifically, we use CALPHAD, density functional theory (DFT), and molecular dynamics (MD) to comprehensively investigate the defect properties of suitable HEAs, offering potential alternatives for future beam windows. We begin by scanning the extensive phase space provided by Cr-Mn-V-Ti-Al-Co HEAs, selecting 8 compositions after evaluating approximately 120,000 unique compositions using CALPHAD. We, then employ DFT-informed machine learning techniques to develop force-field parameters. Finally, MD simulations using these developed force-field parameters will be used to study the effects of radiation damage on the defect and mechanical properties of the selected alloys. This research explains the use of the CALPHAD approach and shows how critical modeling (DFT and MD) is in developing novel material such as HEAs. It also highlights the promising role of machine learning in this field. The results from this study will greatly improve the novel materials development to be used in next-generation accelerator components, leading to higher beam power and longer operational times of BIDs.

43 PARTICLE ACCELERATORS↗