Search NASA⌕ Search

SEARCH · Search NASA

Results for “molecular dynamic simulation”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

A Robotic High-Throughput Grid-Search Platform for Mapping Phase Behavior in Triblock Copolymer–Homopolymer Blends

We present a high-throughput experimental investigation of the phase behavior in triblock copolymers (PS-b-PB-b-PS and PS-b-PI-b-PS) and polystyrene (PS) homopolymer blends as a function of homopolymer molecular weight (MW) and blend ratio. Using a robotic thin-film processing platform (NOVA) integrated with Grazing Incidence Small-Angle X-ray Scattering (GISAXS) and Atomic Force Microscopy (AFM), we systematically mapped the order–disorder transition (ODT) boundaries and domain spacing evolution across a broad MW range (4.0–101.3 kDa) with varying homopolymer loadings (10% to 90%). The results reveal three distinct regimes: low-MW homopolymers, corresponding to the wet-brush regime produced only gradual domain swelling before disordering at high blend ratios (weight fraction); medium-MW homopolymers, corresponding to thedry-brush regime induced significant domain spacing increase up to 80% followed by earlier disordering, while high-MW homopolymers led to macrophase separation with minimal changes in domain spacing. Additionally, coarse-grained molecular dynamics simulations confirmed our experimental finding that in the low-MW region, the PS homopolymer uniformly distributed in the PS domain. These findings demonstrate that homopolymer molecular weight critically governs both the extent of domain swelling and the onset of disorder in triblock copolymer systems. This high-throughput platform enables the rapid mapping of composition–morphology relationships and can be integrated with AI/ML tools for designing next-generation nanostructured polymers.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Conformational Isomerization of Imide Anions Governs Solvation and Transport in Water-in-Salt Electrolytes

The behavior of highly concentrated electrolytes departs radically from the dilute-solution theory, yet the molecular origin of this transformation remains unresolved. Here, we identify the conformational isomerization of molecular ions as a decisive, previously unrecognized control parameter governing structure and transport in crowded aqueous electrolytes. Across a series of fluorosulfonimide anions, we show that increasing concentration drives a collective shift from extended transoid to compact cisoid conformers, revealed by small-angle X-ray scattering, vibrational spectroscopy, pulsed-field gradient NMR, and molecular dynamics simulations. This conformational transition triggers a collapse of the hydrogen-bonded water network and the emergence of densely packed ionic domains with confined water, producing a qualitative change in Li+ transport from solvent-mediated diffusion to network-confined hopping. Anion size and asymmetry systematically tune the onset of this transition, demonstrating that molecular geometry dictates mesoscale organization and dynamics in the ion-rich regime. Our results establish ion conformation, not merely composition or coordination, as a fundamental thermodynamic variable in concentrated solutions, providing a chemical framework that unifies solvation structure and transport in water-in-salt electrolytes and suggesting new principles for designing dense ionic media.

Nguyen, Huong TD↗
NASA NTRS2012

Development and Application of Interatomic Potentials for Ultra High Temperature Ceramics (UHTC): ZrB2 and HfB2

Ultra high temperature ceramics (UHTC) including ZrB2 and HfB2 are characterized by high melting point, good strength, and reasonable oxidation resistance. These materials are of interest for use as sharp leading edges for hypersonic vehicles among other applications. Progress in computational modeling of UHTCs has been limited in part due to the absence of suitable interatomic potentials. We present a Tersoff style parameterization of such potentials for ZrB2 and HfB2 appropriate for atomistic simulations. Parameters are fit to data generated from ab initio calculations. The accuracy of the potentials is assessed against further ab initio data. As a first non ]trivial application, molecular dynamics simulations are performed to evaluate the thermal conductivity of single crystals and the thermal resistance of high symmetry grain boundaries.

Lawson, John W.↗
DOE OSTI2025

Entropy-Driven Porous Liquids Allowing Gas Solubility in Solvent-Filled Imine-Based Porous Organic Cages

Porous liquids offer a promising platform for gas separation by combining fluid processability with intrinsic molecular porosity. Traditional Type II porous liquids are formed by dissolving porous molecular cages in size-excluded solvents, limiting solvent options and practical applications. In this work, we introduce a novel method of creating Type II porous liquids using common small solvents, where intrinsic porosity is achieved at elevated pressures due to the selective displacement of solvent molecules by gas molecules within the cage structures. Using molecular simulations, we investigate the behavior of CO 2 in solutions of the imine-based porous organic cage CC13 dissolved in small molecular solvents such as chloroform and 1,2-dimethoxyethane (DME). Grand canonical Monte Carlo simulations of solid-state CC13 reveal that selectivity reversal, where smaller CO 2 molecules displace larger solvent molecules inside the cage, is achievable at sufficiently high pressures. Temperature quench molecular dynamics simulations confirm that while CO 2 displacement within chloroform-filled cages is limited, DME enables entropy-driven cage CO 2 occupancy at pressures as low as ∼23 bar, setting up the foundation of an alternative way of forming Type II porous liquids.

adsorption↗
DOE OSTI2025

The Work of Mechanical Degradation in Elongating Polymer Melts

Molecular dynamics simulations are used to study the mechanical degradation of well-entangled polymer melts during uniaxial extensional flow. Simulations measure the transient rise in extensional stresses and relate them to the molecular alignment and scission of chain backbones. Intermolecular entanglements couple chain scission in space and time, making degradation sensitive to deformation history and strain rate in ways not displayed by dilute polymer solutions. The rate of chain scission is nonmonotonic and peaks at strains corresponding to the maximum extensibility of entanglement segments but prior to the full extension of chain backbones. We measure a specific work per scission event w* and decompose it into separate contributions associated with chain alignment, chemical bond breaking, and scission-induced plasticity. We find chain scission in melts requires activating plastic dissipation that is multiple orders of magnitude larger than the chemical work required to break a covalent backbone bond. Our findings underscore the critical need to consider bulk polymer mechanics and rheology in designing efficient mechanical degradation and mechanochemical processes.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Scaling Field-Theoretic Simulation for Multicomponent Mixtures with Neural Operators

Multicomponent polymer mixtures are ubiquitous in biological self-organization but are notoriously difficult to study computationally. Plagued by both slow single molecule relaxation times and slow equilibration within dense mixtures, molecular dynamics simulations are typically infeasible at the spatial scales required to study the stability of mesophase structure. Polymer field theories offer an attractive alternative, but analytical calculations are only tractable for mean-field theories and nearby perturbations, constraints that become especially problematic for fluctuation-induced effects such as coacervation. Here, we show that a recently developed technique for obtaining numerical solutions to partial differential equations based on operator learning, neural operators, lends itself to a highly scalable training strategy by parallelizing per-species operator maps. We illustrate the efficacy of our approach on six-component mixtures with randomly selected compositions and that it significantly outperforms the state-of-the-art pseudospectral integrators for field-theoretic simulations, especially as polymer lengths become long.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

From 2D to 4D: a containerized workflow and browser to explore dynamic chromatin architecture

Background Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two-dimensional (2D) genome-wide contact maps of chromatin interactions by capturing the spatial proximity between genomic loci, which reveal interaction frequencies but lack the spatial resolution needed to interpret the three-dimensional (3D) genome structure(s). Emerging evidence suggests that epigenetic regulation is closely linked to 3D genome architecture, and that structural changes over time (4D) drive key biological processes in development, disease, and environmental response. Thus, integrating 3D structure with functional data is critical for a more complete understanding of genome regulation. Previous work, most notably the 4DHiC chromosome modeling framework, has shown that physical multi-dimensional modeling approaches rooted in polymer physics and molecular dynamics can resolve these structures at biologically meaningful resolutions by integrating temporal Hi-C data with physical constraints to uncover dynamic chromosome reorganization. Thus, molecular dynamics simulations, constrained by Hi-C contact matrices, can resolve fine-scale structural changes and reveal functionally significant transitions in chromatin conformation. Results Herein, we present the 4D Genome Browser Workflow (4DGBWorkflow) and the 4D Genome Browser (4DGB). The algorithm is based on the 4DHiC method, and the containerized tool is an end-to-end workflow that can transform, filter, and view 4D epigenomics and chromatin datasets, allowing non-specialists to apply three-dimensional modeling principles to diverse datasets and experimental conditions. The software executes on a laptop running macOS, Linux or Windows. From input Hi-C files (.hic), the 4DGBWorkflow produces 3D reconstructions of chromosomes, integrates the reconstruction with track data (e.g., epigenetic marks, transcriptome profiles), and provides comparative visualization of the results in a single workflow. Conclusions The 4DGBWorkflow and 4D Genome Browser are open-source tools for comparative analysis and visualization of 4D chromosome datasets, including chromatin architecture and epigenomic signals. Automatic integration of Hi-C data with molecular dynamics democratizes the construction of time resolved 3D genome structures, simplifying complex simulations and data integration schemes.

3D Genome Browser↗
NASA NTRS2009

Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations

Atomistic models of epoxy polymers were built in order to assess the effect of structure at the nanometer scale on the resulting bulk properties such as elastic modulus and thermal conductivity. Atomistic models of both bulk polymer and carbon nanotube polymer composites were built. For the bulk models, the effect of moisture content and temperature on the resulting elastic constants was calculated. A relatively consistent decrease in modulus was seen with increasing temperature. The dependence of modulus on moisture content was less consistent. This behavior was seen for two different epoxy systems, one containing a difunctional epoxy molecule and the other a tetrafunctional epoxy molecule. Both epoxy structures were crosslinked with diamine curing agents. Multifunctional properties were calculated with the nanocomposite models. Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between the carbon nanotube and the surrounding epoxy matrix. These estimated values were used in a multiscale model in order to predict the thermal conductivity of a nanocomposite as a function of the nanometer scaled molecular structure.

Hinkley, J.A.↗
DOE OSTI2024

Ab-initio molecular dynamics study of eutectic chloride salt: MgCl2–NaCl–KCl

Ionic liquid materials are viable candidates as a heat transfer fluid (HTF) in a wide range of applications, notably within concentrated solar power (CSP) technology and molten salt reactors (MSRs). For next-generation CSP and MSR technologies that strive for higher power generation efficiency, a HTF with wide liquid phase range and energy storage capabilities is crucial. Studies have shown that eutectic chloride salts exhibit thermal stability at high temperatures, high heat storage capacity, and are less expensive than nitrate and carbonate salts. However, the experimental data needed to fully evaluate the potential of eutectic chloride salts as a HTF contender are scarce and entail large uncertainties. Considering the high cost and potential hazards associated with the experimental methods used to determine the properties of ionic liquids, molecular modeling can be used as a viable alternative resource. In this study, the eutectic ternary chloride salt MgCl 2 –NaCl–KCl is modeled using ab-initio molecular dynamics simulations (AIMDs) in the liquid phase. Using the simulated data, the thermophysical and transport properties of eutectic chloride salt can be calculated: density, viscosity, heat capacity, diffusion coefficient, and ionic conductivity. For an initial model validation, experimental pair-distribution function data were obtained from X-ray total scattering techniques and compared to the theoretical pair-distribution function. Additionally, theoretical viscosity values are compared to experimental viscosity values for a similar system. The results provide a starting foundation for a MgCl 2 –NaCl–KCl model that can be extended to predict other fundamental properties.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2026

Solvent effects on triplet yields in BODIPY-based photosensitizers

Here, we employ molecular dynamics simulations and quantum rate theories to elucidate the complex condensed-phase dynamics underpinning triplet-state formation in organic photosensitizers. Using models informed by first-principles calculations complete with a molecular representation of solvents of different polarities, we elucidate the interplay of the internal and environmental interactions underlying triplet yield. We find that triplet yields depend sensitively on the dielectric stabilization of the charge transfer intermediate that facilitates a transition into the triplet manifold. Our results illustrate the importance of molecularly detailed models in understanding the excited-state internal charge-transfer dynamics of photochemically relevant organic molecules.

Coello Escalante, Leonardo [University of Californ↗
NASA NTRS1999

Computer Simulation Studies of Ion Channel Gating: Characteristics of the M2 Channel of Influenza-A Virus in a Phospholipid Bilayer

The 25 amino acids long, transmembrane fragment of the Influenza virus M2 protein forms a homotetrameric channel that transports protons across lipid bilayers. It has been postulated that high efficiency and selectivity of this process is due to gating by four histidine residues that occlude the channel lumen in the closed state. Two mechanisms of gating have been postulated. In one mechanism, the proton is "shuttled" through the gate by attaching to the delta nitrogen atom on the extracellular side of the imidazole ring, followed by the release of the proton attached to the epsilon nitrogen atom on the opposite side. In the second mechanism, the four histidines move away from each other due to electrostatic repulsion upon protonation, thus opening the gate sufficiently that a wire of water molecules can penetrate the gate. Then, protons are transported by "hopping" along the wire. In this paper, both mechanisms are evaluated in a series of molecular dynamics simulations by investigating stability of different protonation states of the channel that are involved in these mechanisms. For the shuttle mechanism, these are states with all epsilon protonated histidines, one biprotonated residue or one histidine protonated in the delta position. For the gate opening mechanism, this is the state in which all four histidines are biprotonated. In addition, a state with two biprotonated histidines is considered. For each system, composed of the protein channel embedded in phospholipid bilayer located between two water lamellae, a molecular dynamics trajectory of approximately 1.3 ns (after equilibration) was obtained. It is found that the states involved in the shuttle mechanism are stable during the simulations. Furthermore, the orientations and dynamics of water molecules near the gate are conducive to proton transfers involved in the shuttle. In contract, the fully biprotonated state, implicated in the gate opening mechanism, is not stable and the channel looses its structural integrity. If only two histidines are biprotonated the channel deforms but remains intact with the gate mostly closed. In summary, the results of this study lend support to the shuttle mechanism but not to the gate opening mechanism of proton gating in M2.

Schweighofer, Karl J.↗
DOE OSTI2025

Molecular Simulation of Functionalized Covalent Organic Framework Membranes for Inorganic Salt Separation

Covalent organic frameworks (COFs) enable molecular-level design of nanochannels for selective separation in pressure-driven membrane processes. Through variation of building blocks and, subsequently, the pore structure and chemistry, membrane performance can be tailored. This study employs nonequilibrium molecular dynamics simulations to theoretically demonstrate the tunable selectivity of COF membranes through a bottom-up functionalization approach. Water and salt transport are evaluated for six β-ketoenamine-linked COFs with varying multilayer thicknesses. For the thinnest multilayer (0.64–0.72 nm), all COFs exhibit low sodium sulfate (Na 2 SO 4 ) rejection (55–66%). However, 20 stacked sheets (6.4–7.2 nm) provide 67–98% rejection, with the sulfonated COF providing the highest Na 2 SO 4 rejection. Analysis of time-resolved ion density profiles reveals that solute rejection is primarily governed by interfacial exclusion arising from pore size and functional group chemistry. Although increasing salt rejection compromises water permeance, the permeance of all COF membranes is at least two orders of magnitude greater than that of a commercially available nanofiltration membrane. Overall, this work guides the rational design of COF membranes for aqueous salt separation.

Nanofiltration↗
DOE OSTI2025

All-Atom Modeling and Simulation of Biopolymer Interface: Dual Role of Antifouling Polymer Brushes

Antifouling polymer brushes are well-known for their exceptional resistance to unwanted protein adsorption. While experimental studies have extensively characterized protein–polymer brush interactions, computational investigations remain limited, largely due to the challenges in accurately modeling and integrating these complex, multicomponent systems without resorting to oversimplification. To address this challenge, this study presents one of the most comprehensive and realistic model systems to date, comprising the substrate, grafted polymers, and proteins. Our work interprets the interactions between polymer brush and protein based on realistic modeling without simplification. In particular, this study utilizes molecular modeling and simulation of polycationic and polyzwitterionic brushes─poly(dimethylaminoethyl methacrylate) (PDMAEMA), poly(2-(N-oxide-N,N-dimethylamino)ethyl methacrylate) (PNOMA), and poly(2-(N-3-sulfopropyl-N,N-dimethylammonium)ethyl methacrylate) (PSBMA)─grafted onto α-quartz substrates via polymerization initiator linkers. The brush models were developed to closely replicate experimentally synthesized samples and to provide detailed insights into structural and dynamical changes at the molecular level during protein adsorption. Using steered molecular dynamics simulations, we show that the PSBMA brush, due to its high local density, exhibits the greatest resistance to protein insertion. Cα root-mean-square deviation and interaction pattern analyses further reveal that the PSBMA brush also induces the most significant destabilization of lysozyme, while the PDMAEMA brush enhances protein stability through ion-mediated interactions. The PNOMA brush, while requiring the lowest force for protein adsorption, induces greater protein destabilization than the PDMAEMA brush, primarily due to electrostatic repulsion caused by a short carbon spacer length. Hydration analysis reveals that both the PSBMA brush and the lysozyme interacting with it exhibit the most rapid dehydration, attributed to the brush’s high local chain density, which results in the greatest lysozyme destabilization and the highest adsorption force. These findings highlight the dual role of antifouling polymer brushes: resisting protein adsorption and modulating protein structural dynamics. In conclusion, this study provides valuable insights for the rational design of next-generation antifouling materials and offers a framework for realistic model development in complex multicomponent systems.

Adsorption↗
DOE OSTI2025

Cluster-Graph Fingerprinting: A Framework for Quantitative Analysis of Machine-Learned Interatomic Model Training and Simulation Data

Machine-learned interatomic models represent a significant advancement in simulation methods, extending the predictive ability of first-principles methods to previously inaccessible length and time scales. However, the data-driven nature of these models can lead to difficult-to-detect errors that can compromise prediction accuracy. To address this challenge, we introduce a novel fingerprinting approach based on the Chebyshev Interaction Model for Efficient Simulation (ChIMES) ML-IAM graph-based descriptor. Our strategy enables efficient and statistically rigorous analysis of system configurations used in ML-IAM training and those generated by their application, e.g., in molecular dynamics simulations. We demonstrate that these fingerprints can effectively assess novelty of a configuration relative to an existing data set and determine dissimilarity among individual configurations, which are two key tasks in workflows for active learning-based ML-IAM training, data set curation, and on-the-fly uncertainty quantification.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Solubilization of PET in binary mixtures of HFIP and DCM

The dissolution of polyethylene terephthalate (PET) is a critical step for a solvent-based process, yet it typically requires highly corrosive or toxic solvents. Here, we investigate the solubilization and conformational behavior of PET in binary mixtures of hexafluoro-2-propanol (HFIP) and dichloromethane (DCM) as a strategy to reduce HFIP usage while maintaining effective dissolution. Small-angle neutron scattering (SANS) measurements reveal that PET remains molecularly dissolved in HFIP/DCM mixtures up to 50 vol% DCM. Analysis of PET chain conformations shows a transition from Gaussian behavior at low HFIP fractions to more swollen chains at intermediate compositions, accompanied by a counter-intuitive minimum in the radius of gyration at 50% HFIP. Complementary SANS measurements of the binary solvents demonstrate that compositional heterogeneity is maximized at this same solvent composition, suggesting a direct coupling between solvent microstructure and polymer dimensions. Molecular dynamics simulations corroborate the experimental findings, revealing solvent domain formation, preferential solvation of PET by HFIP, and a “caging” effect arising from solvent heterogeneity that leads to polymer coil compaction. Together, these results provide molecular-level insight into polymer behavior in mixed solvent systems and establish HFIP/DCM mixtures as a promising, more sustainable solvent platform for the PET post-process.

Arifuzzaman, Arif [ORNL]↗
DOE OSTI2025

Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF‐Trap

The constant fragment (Fc) of the immunoglobulin G1 (IgG1) subtype is increasingly recognized as a crucial scaffold in the development of advanced therapeutics due to its enhanced specificity, efficacy, and extended half‐life. A prime example is VEGF‐Trap (Aflibercept), a recombinant fusion protein that merges the Fc region of the IgG1 subtype with the binding domains of vascular endothelial growth factor receptors (VEGFR)‐1 and VEGFR‐2. The Fc region's role in N‐glycosylation is particularly important, as it significantly influences protein stability. Herein, the first near‐physiological temperature structures of the N‐glycan‐bound Fc fragment of IgG1 subtype from a biosimilar VEGF‐Trap are presented, determined using the SPring‐8 Angstrom Compact free electron LAser (SACLA) and the Turkish Light Source (Turkish DeLight). Comparative analysis with cryogenic structures, including existing data, reveals alternate conformations within the glycan‐binding pocket. Furthermore, molecular dynamics simulations indicate the presence of a high degree of structural plasticity, explaining how the protein adapts its structure through conformational changes. The observed structural fluctuations/conformational changes demonstrate the effect of N‐glycans on protein stability. These findings offer new insights into the molecular basis of Fc‐mediated functions and provide valuable information for the design of next‐generation therapeutics.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1993

Molecular dynamics of interface rupture

Several situations have been studied in which a fluid-vapor or fluid-fluid interface ruptures, using molecular dynamics simulations of 3000 to 20,000 Lennard-Jones molecules in three dimensions. The cases studied are the Rayleigh instability of a liquid thread, the burst of a liquid drop immersed in a second liquid undergoing shear, and the rupture of a liquid sheet in an extensional flow. The late stages of the rupture process involve the gradual withdrawal of molecules from a thinning neck, or the appearance and growth of holes in a sheet. In all cases, it is found that despite the small size of the systems studied, tens of angstroms, the dynamics is in at least qualitative accord with the behavior expected from continuum calculations, and in some cases the agreement is to within tens of percent. Remarkably, this agreement occurs even though the Eulerian velocity and stress fields are essentially unmeasurable - dominated by thermal noise. The limitations and prospects for such molecular simulation techniques are assessed.

Koplik, Joel↗