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DOE OSTI2026

Microstructure, Transport, and Mechanics of Compacted Clay Simulated at the 0.1 μm Scale (1400 Smectite Clay Particles) Using a Coarse-Grained Model with Explicit Counterions

Clay-rich geomaterials play a critical role in many subsurface systems. The macroscale properties of these materials (low permeability, high ionic conductivity, high swelling pressure, etc.) are sensitive to molecular-level adsorption and hydration interactions at clay−water interfaces. Efforts to develop multiscale simulation approaches to predict these properties reveal a scale gap between atomistic simulations (typically limited to systems smaller than 10 nm) and continuum-scale models (which use computational grid elements with dimensions ≳ 10 μm). In this study, we present a coarse-grained (CG) framework that partly bridges this gap by simulating compacted smectite clay assemblages with dimensions of 0.1 μm containing 1,400 clay particles across a range of dry densities (1,050 to 1,850 kg·m −3 ) and Na/Ca counterion compositions (Na fraction ranging from 0.2 to 1). The simulated systems, along with their reconstructed binary three-dimensional pore networks, are used to evaluate the microstructure, pore size distribution, tortuosity, ion diffusivity, and swelling pressure of compacted smectite clay. Results show that our approach captures important features of the mesoscale heterogeneity of compacted clays, including tactoid formation, hierarchical porosity, and anisotropic pore networks. Results also reveal how compaction and counterion composition govern emergent behaviors, including dominant pore sizes, directional transport, and electrochemical response. This work highlights the potential of CG simulations to bridge molecular and continuum scales and to advance geotechnical and environmental applications involving clay-rich materials as well as related nanoporous media such as geopolymers and calcium-silicate-hydrate. However, the results also suggest that accurate prediction of certain microstructural and mechanical properties (e.g., swelling pressure) may require even larger-scale systems on the order of 1 μm.

02 PETROLEUM↗

DOE OSTI2024

Molecular Dynamics Study of the Effect of Grafting Density on Ion Diffusivity in a MARTINI Coarse-Grained Strong Polyelectrolyte Brush

Because surface-grafted polyelectrolyte brushes (PEBs) are responsive to external stimuli, such as electric fields and ionic strength, PEBs are attractive for applications ranging from drug delivery to separation technologies. Essential to PEB utilization is understanding how critical parameters like grafting density (σ) impact the PEB structure and the dynamics of the PEB and counterions. To study the effect of σ on PEB and the counterion structure and dynamics, we fine-tune a coarse-grained model that retains the chemical specificity of a strong polyelectrolyte, poly[(2-(methacryloyloxy)ethyl) trimethylammonium chloride] (PMETAC), using the MARTINI force field. Using “salt-free” conditions where the counterion concentration balances the charge on the brush, we build coarse-grained (CG) molecular dynamics simulations for MARTINI PMETAC brushes (N = 150 monomers; M W = 31.2 kg/mol) at experimentally relevant values of σ = 0.05, 0.10, 0.20, and 0.40 chains/nm 2 . Using 5 μs simulations, we investigate the effects of grafting density on the PEB structure, ion dissociation dynamics, polymer mobility, and counterion diffusivity. Results show that competition between electrostatic interactions, steric hindrance, and polymer mobility controls counterion diffusivity. Finally, the interplay of these factors leads to diffusivity that depends non-monotonically on σ, with counterion diffusivity peaking at an intermediate σ = 0.10 chains/nm 2 .

36 MATERIALS SCIENCE↗

DOE OSTI2026

The Complexation Properties of Self-Defensive Microgel-Modified Antimicrobial Surfaces

The complexation of cationic antimicrobials with polyanionic microgels on a biomaterial surface can render that surface self-defensive against bacteria by killing those bacteria which physically contact the antimicrobial-loaded microgels. This killing has been attributed to the contact-driven transfer of antimicrobial from a microgel to a challenging bacterium, though much remains unknown about this process. Here, in this study, we use a combination of experiments and computational modeling to identify key aspects of the complexation phenomena which influence the self-defensive properties. We synthesize poly(acrylic acid) (PAA) microgels (∼2–5 μm diameter) via membrane emulsification and electrostatically deposit them onto polycaprolactone (PCL) coupons or onto glass to form a discontinuous submonolayer. Subsequent microgel loading with colistin or with Sub5 antimicrobial peptide (AMP) causes microgel deswelling. Under physiological conditions Sub5 remains stably sequestered whereas colistin is quickly released. Coarse-grained molecular dynamics (CGMD) simulations confirm stronger Sub5/PAA complexation. CGMD calculations also indicate that Sub5 forms dimers and higher-order structures, a prediction confirmed experimentally by Small-Angle X-ray Scattering (SAXS). Supramolecular structure entropically enhances the complexation strength because of enhanced counterion release per complexation event, and this finding can help identify other antimicrobials well suited for such a nonelutive yet self-defensive strategy. CGMD simulations also show that Sub5 has a higher complexation strength with the Staphylococcus aureus membrane than it does with PAA, confirming that there is a thermodynamic driving force for antimicrobial transfer. Such self-defensive surfaces significantly reduce S. aureus colonization (over 90% reduction relative to unmodified controls) in an in vitro hematogenous contamination model and remain cyto-compatible as evidenced by mesenchymal stem cell spreading and proliferation.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Enhanced Interfacial Bonding of Graft Copolymers

To understand how thermoplastic welding strength can be tuned through chemical modifications and macromolecular topology, we combined coarse-grained molecular dynamics (MD) simulations with experimental validation. Our simulations examined the diffusion dynamics of both linear and graft polymers across representative interfaces, revealing that diffusion-controlled interdigitation follows a power law, with the exponent decreasing from 0.34 to 0.11 as grafting density increases from 7.5 to 196% (with side chains grafted to both sides of a monomer unit). The addition of side chains enhances welding efficiency, as dense bottlebrush polymers with high grafting density reach maximum rupture strength faster than linear polymers. However, their saturated rupture strength is lower. This observation is subsequently corroborated by experimental lap-shear tests comparing linear polyethylene with octene grafted polyethylene elastomers. Our MD simulations show that unlike linear polymers, where backbone entanglements dominate, the grafted side chains introduce mechanisms in addition to entanglement dilution. The rapid interdigitation of side chains creates a dense mesh of entropic van der Waals contacts, which can also enhance the film welding. Furthermore, our MD simulations reveal a brittle rupture behavior in linear and comb-like (mildly grafted) polymers, while bottlebrush (densely grafted) polymers display elastomeric behavior with a pronounced stress plateau prior to fracture. Our simulations deconvolute the influence of polymer topology on deformation behavior. The rate of polymer deformation becomes lower than the applied strain rate prior to rupture, and the onset of this deviation is progressively delayed from linear to bottlebrush polymers. This trend highlights the critical role of molecular architecture in governing the mechanical response. In conclusion, these results provide deeper insight into the underlying welding mechanisms of topological polymers and present a potential approach for mitigating the interface anisotropy that is inherent in advanced manufacturing techniques such as fused filament fabrication.

graft copolymers↗

DOE OSTI2025

Nanoscale Miscibility in In Situ Polymerized Hybrid Electrolytes Speeds Up Ion Dynamics and Enables Stable Cycling of Li Metal Batteries

While the potential use of copolymerized electrolytes in Li metal batteries is subject to intense investigation, the fundamental understanding of the nanoscale domain formation and its effect on Li + transport is still lacking. In this study, we investigated the correlation between the Li + transport mechanism and the miscibility of monomers in polymer blend electrolytes derived from the in situ copolymerization of methyl methacrylate (MMA) and vinylene carbonate (VC) in the presence of polyethylene glycol dimethyl ether (PEGDME) plasticizer and bis(trifluoromethanesulfonyl)imide (LiTFSI) salt. The addition of a polar short chain plasticizer reduced the dynamic and structural heterogeneities of the electrolyte. Small-angle X-ray scattering (SAXS) measurements and coarse-grained molecular dynamics (MD) simulations were used to investigate the nanoscale structure of the electrolytes. The distribution of relaxation times corresponding to the three distinct diffusion mechanisms of the free and interfacial Li + ions at the copolymer/plasticizer and electrolyte/SEI boundaries was analyzed in a broad temperature range to elucidate the Li + transport mechanism. Furthermore, the chemical composition of the SEI and the contribution of a ceramic lithium lanthanum zirconium oxide (LLZO, Li 7 La 3 Zr 2 O 12 ) phase on the interfacial resistance, salt degradation, and SEI stability were studied by X-ray photoelectron spectroscopy (XPS) depth profile analysis and electrochemical testing.

Li metal↗

DOE OSTI2025

Closed-Loop Control of Active Nematic Flows

Stabilizing and shaping autonomous flows of active fluids is a fundamental challenge and a prerequisite for applications. We embed a light-responsive microtubule-based nematic in a proportional-integral control loop that adjusts the applied light intensity in response to real-time measurements of the spatially averaged flow speed. The self-regulating hardware-software-wetware system maintains a target flow speed against external or internal perturbations, including protein aging and aggregation, sample-to-sample variability, and temperature variation. Varying the controller’s gains reveals antagonistic roles between feedback and intrinsic processes, leading to nontrivial dynamics observed in fluctuation spectra. In particular, oscillations emerge from the interplay between the controller, motor binding kinetics, and active hydrodynamic relaxation. Accounting for the underlying binding timescale, our coarse-grained model and nematohydrodynamics simulations corroborate these observations. This work provides insight into the coupled dynamics of controlled active matter, laying the foundation for spatiotemporal patterning of active stress to generate and stabilize new dynamical configurations.

Active nematics↗

DOE OSTI2025

Structured interactions drive abrupt transitions in the spatial organization of microbial communities

Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Some of these mechanisms are species specific and enable cells to modulate their movement based on the ecological identity of neighboring species. Here, we introduce a model in which bacteria interact via local signals that either enhance or suppress the motility of neighboring cells depending on species type. Through large-scale simulations and a coarse-grained stochastic model, we demonstrate the emergence of a sharp transition driven by nucleation processes: increasing the density of motility-suppressing interactions drives the system from a fully mixed, motile phase to a state characterized by large, stationary bacterial clusters. Remarkably, in systems with a large number of interacting species, this transition can be triggered solely by altering the structure of the motility-regulation interaction matrix while maintaining species and interaction densities constant. In particular, we find that heterogeneous and modular interactions promote the transition more readily than homogeneous random ones. These findings add a dimension to the theory of motility-induced phase separation and contribute to the ongoing effort to understand microbial interactions, suggesting that structured, nonrandom ones may be key to reproducing commonly observed spatial patterns in microbial communities.

bacterial communities↗

DOE OSTI2025

Closed-loop control of active nematic flows

Stabilizing and shaping autonomous flows of active fluids is a fundamental challenge and a prerequisite for applications. We embed a light-responsive microtubule-based nematic in a proportional-integral control loop that adjusts the applied light intensity in response to real-time measurements of the spatially averaged flow speed. The self-regulating hardware/software/wetware system maintains a target flow speed against external or internal perturbations, including protein aging and aggregation, sample-to-sample variability, and temperature variation. Varying the controller’s gains reveals antagonistic roles between feedback and intrinsic processes, leading to nontrivial dynamics observed in fluctuation spectra. In particular, oscillations emerge from the interplay between the controller, motor binding kinetics, and active hydrodynamic relaxation. Accounting for the underlying binding timescale, our coarse-grained model and nematohydrodynamics simulations corroborate these observations. This work provides insight into the coupled dynamics of controlled active matter, laying the foundation for spatiotemporal patterning of active stress to generate and stabilize new dynamical configurations.

Nishiyama, Katsu [Brandeis Univ., Waltham, MA (Uni↗

NASA NTRS2022

Resolving the fine structure in the energy landscapes of repeat proteins

Ankyrin (ANK) repeat proteins are coded by tandem occurrences of patterns with around 33 amino acids. They often mediate protein–protein interactions in a diversity of biological systems. These proteins have an elongated non-globular shape and often display complex folding mechanisms. This work investigates the energy landscape of representative proteins of this class made up of 3, 4 and 6 ANK repeats using the energy-landscape visualisation method (ELViM). By combining biased and unbiased coarse-grained molecular dynamics AWSEM simulations that sample conformations along the folding trajectories with the ELViM structure-based phase space, one finds a three-dimensional representation of the globally funnelled energy surface. In this representation, it is possible to delineate distinct folding pathways. We show that ELViMs can project, in a natural way, the intricacies of the highly dimensional energy landscapes encoded by the highly symmetric ankyrin repeat proteins into useful low-dimensional representations. These projections can discriminate between multiplicities of specific parallel folding mechanisms that otherwise can be hidden in oversimplified depictions.

Murilo N. Sanches↗

DOE OSTI2026

A lumped particle direct simulation Monte-Carlo method combined with the collisional-radiative model for simulations of non-equilibrium laser-induced plasma plumes

Collisional plasma plumes induced by laser irradiation of material targets exhibit large variations in local density as well as ionization and excitation states, making purely hydrodynamic or kinetic simulations inaccurate or infeasible. To address this challenge and capture non-equilibrium effects in laser-induced plasma plumes at arbitrary degrees of ionization, we develop a hybrid computational approach that combines the kinetic direct simulation Monte Carlo (DSMC) method with a collisional-radiative model (CRM). This ℓDSMC-CRM approach utilizes a lumped particle method to represent minor fractions of excited ions in particle-based simulations and a special coarse-graining technique for atomic spectra and photoionization rates, ensuring numerical convergence at reduced computational cost. The hybrid approach is applied to simulate spatially homogeneous relaxation as well as one- and two-dimensional expansions of plasma plumes induced by irradiation of a copper target by a nanosecond laser pulse in a vacuum or background gas. The comparison with an equilibrium model, where local Saha-Boltzmann equilibrium is enforced, shows that the non-equilibrium effects play a dominant role. The equilibrium model can fail to predict the flow structure and strongly underestimate the degree of absorption of laser radiation by the plume. The ℓDSMC-CRM approach is validated against experimental data demonstrating reasonable agreement with the experimental electron density and temperature, while the equilibrium model is found to dramatically underestimate electron density and temperature. The flexibility of the ℓDSMC-CRM approach allows for its seamless integration into existing DSMC frameworks, making it a valuable tool for high-fidelity plasma modeling in laser-material interactions, laser-based manufacturing, and beyond.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2008

The LHT (Lunar Highlands Type) Regolith Simulant Series

Three NU-LHT (NASA/USGS-Lunar Highlands Type) regolith simulants have been produced to date: NU-LHT-1M, -ID, and -2M. A fourth simulant is currently in production: NU-LHT-3C. The "M" (medium) designation indicates a simulant with a grain size of <1 mm, "D" (dust) a simulant with a grain size of <36 microns, and "C" (coarse) a simulant with a 10 cm maximum particle size. The composition of these simulants is based on a NASA average Apollo 16 regolith chemical composition, However, the mixing model used to create our simulants is based on cationic nonnative mineral proportions derived from the target chemical composition to approximate lunar modal mineralogy rather than chemical composition per se. Accordingly, the amount of plagioclase, pyroxenes, olivine, and trace minerals in the simulant crystalline fraction approximates that of the lunar regolith. We also added synthetic agglutinate in amounts approximate for low-medium regolith maturity. A pure glass fraction was also added to simulate other types of lunar glasses present in the regolith. In addition, the 3C simulant will include synthetic impact melt breccia clasts for the >1 cm particles. The bulk raw materials used to create these simulants include clinopyroxene-norite, anorthosite, hartzburgite and noritic mill waste from the Stillwater Mine, Nye, MT, and olivine from the Twin Sisters dunite, WA. Added trace minerals include beach sand ilmenite, chromite, synthetic p-tricaicium phosphate (whitiockite), gem grade fluor-apatite, and pyrite. The agglutinate, glasses, and synthetic breccia were designed and prepared at an industrial plasma melting facility in Boulder, CO, using Stillwater mill waste feedstock for the melt. These simulants do not include nanophase-feO. The M and C simulant grain size distribution (down to 0.4 microns) approximates that of Apollo 16 regolith and the regolith in general.

Stoeser, Douglas↗

DOE OSTI2025

COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Correction to “COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins”

Molecular interactions↗

DOE OSTI2025

Investigating the Effect of Water on the Mechanical Properties of Cellulose from Multiscale Molecular Dynamics Simulations

Classical molecular dynamics (MD) simulations provide insight into the structure and physicochemical properties of materials with atomic resolution. However, the length and time scales accessible to atomistic MD are orders of magnitude smaller than many relevant processes such as the response of a bulk material to experimentally accessible strain rates, which presents challenges when comparing models to experimental measurements. Bottom-up coarse-graining provides a means for systematically mapping atomistic information to lower resolution models to increase the length and time scales achievable by simulation. Cellulose is an abundant carbohydrate biopolymer with applications to many fields of research, such as materials science and renewable energy, due to its desirable mechanical properties and viability for conversion into biofuel. The effect of moisture content on the Young's modulus of cellulose is of special interest due to its native environment often being in the hydrated secondary plant cell wall and the grinding energy requirements for biomass feedstock preprocessing. The current work investigates the effects of water solvent on the Young's modulus of cellulose calculated from coarse-grained MD mechanical stress simulations. The coarse-grained model was parametrized from atomistic MD calculations of cellulose-cellulose potentials of mean force using umbrella sampling techniques under vacuum and solvated conditions. The Young's moduli of the coarse-grained cellulose assemblies parametrized from cellulose in vacuum or solvated in water were computed via mechanical stress simulations to highlight the importance of capturing solvent interactions for modeling the mechanical behavior of cellulose.

BASIC BIOLOGICAL SCIENCES,RADIATION PROTECTION AND↗

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↗

NASA NTRS1993

Use of networked workstations for parallel nonlinear structural dynamic simulations of rotating bladed-disk assemblies

The principal objective of this research is to investigate, develop and demonstrate coarse-grained, parallel-processing strategies for nonlinear dynamic simulations for rotating bladed-disk assemblies. The parallel -processing strategies addressed include numerical algorithms for parallel nonlinear solutions and techniques to effect load balancing among processors. The parallel environment employed is a distributed-memory, coarse-grained one consisting of networked workstations. A parallel explicit time integration method has been implemented for transient nonlinear solutions of rotationg bladed-disk assemblies. Automatic domain partitioning techniques have been investigated for load balancing among processors. Advanced computing environments, data structures and interactive computer graphics all contribute to an integrated parallel finite element analysis system to facilitate more efficient and powerful dynamic simulations.

Hsieh, Shang-Hsien↗

DOE OSTI2026

Challenges of conventional iterative all-atom and coarse-grained multiscale molecular dynamics

In this work, we evaluate the biomolecular dynamics behaviors when conventionally iterating between all-atom (AA) and coarse-grained (CG) molecular dynamics (MD) simulations over multiple cycles. We implemented the workflow to iterate between AA and CG in OpenMM, namely the iterative multiscale MD (iMMD) simulation workflow. In particular, we aim to identify practical applications for iterating between AA and CG simulations in a conventional manner without any constraints or model modifications. We evaluate the iMMD workflow on four representative systems, spanning folding of two soluble proteins and protein-protein as well as protein-lipid interactions of two membrane proteins. We observe that iteration between AA and CG representations could help the soluble proteins exit undesirable metastable states to fold, resulting from random protein structural distortions due to cycling. Consequently, the most reliable use of iterative AA and CG simulations appears to be to accelerating complex lipid mixing for membrane-bound protein systems rather than sampling protein conformational space. Our work explores the practical usages and limitations for iterative AA and CG simulations using readily available AA and CG force fields. The evaluated iMMD workflow in OpenMM is made available at https://github.com/lanl/iMMD.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Molecular Mechanisms Underlying Surfactant-Based Plastics De-Inking

Surfactant-mediated binder removal is critical for de-inking pretreatment in plastics recycling, yet the molecular mechanisms governing surfactant performance remain poorly understood. We used all-atom (AA) and coarse-grained (CG) molecular dynamics (MD) simulations alongside alkaline surfactant washing experiments to investigate interactions between a series of surfactants and a polyether urethane (PEU) binder in solution and on a polyethylene (PE) surface. Experiments reveal a range of de-inking efficiencies, ranging from <25 to >95% depending upon surfactant headgroup charge and tail length. AA simulations reveal that charged surfactants reach stable levels of surfactant coverage, while nonionic surfactants aggregate on the binder. CG umbrella sampling calculations quantify the thermodynamics of binder desorption in water. In ∼0.25 M surfactant solutions, up to a 52% reduction in the free energy barrier is computed, with trends in good agreement (R 2 = 0.92, Pearson’s r = –0.96, Spearman’s ρ = –0.83) with experimental de-inking efficiencies. We find that charged surfactants are more effective than nonionic surfactants for de-inking and propose three regimes of surfactant de-inking processes: good de-inking occurs in surfactants that promote PEU desorption with a low radius of gyration (R g ); moderate de-inking occurs when surfactants stabilize PEU but increase R g ; poor de-inking occurs in surfactants that aggregate on the binder and promote extensive anchoring to the surface. Overall, these molecular-level insights have the potential to guide the design of surfactant formulations for plastics recycling applications.

ink removal↗