Search NASA⌕ Search

SEARCH · Search NASA

Results for “molecular dynamics (MD)”

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 199 records · Page 11

Accelerated Sequence Design of Star Block Copolymers: An Unbiased Exploration Strategy via Fusion of Molecular Dynamics Simulations and Machine Learning

Star block copolymers (s-BCPs) have potential applications as novel surfactants or amphiphiles for emulsification, compatibilization, chemical transformations, and separations. s-BCPs have chain architectures where three or more linear diblock copolymer arms comprised of two chemically distinct linear polymers, e.g., solvophobic and solvophilic chains, are covalently joined at one point. The chemical composition of each of the subunit polymer chains comprising the arms, their molecular weights, and the number of arms can be varied to tailor the surface and interfacial activity of these architecturally unique molecules. Further, this makes identification of the optimal s-BCP design nontrivial as the total number of plausible s-BCP architectures is experimentally or computationally intractable. In this work, we use molecular dynamics (MD) simulations coupled with a reinforcement learning-based Monte Carlo tree search (MCTS) to identify s-BCP designs that minimize the interfacial tension between polar and nonpolar solvents. We first validate the MCTS approach for the design of small- and medium-sized s-BCPs and then use it to efficiently identify sequences of copolymer blocks for large-sized s-BCPs. The structural origins of interfacial tension in these systems are also identified by using the configurations obtained from MD simulations. Chemical insights into the arrangement of copolymer blocks that promote lower interfacial tension were mined using machine learning (ML) techniques. Overall, this work provides an efficient approach to solve design problems via fusion of simulations and ML and provides important groundwork for future experimental investigation of s-BCPs for various applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Computational and experimental study of different brines in temperature swing solvent extraction desalination with amine solvents

Rapid global urbanization and high-salinity wastewater disposal from industrial activities have exerted significant pressure on water resources. Over the past few years, temperature swing solvent extraction (TSSE) has been identified as a promising technique to desalinate hypersaline brines. Despite its potential, the TSSE desalination literature has been mainly based on empirical insights, and the limited molecular simulation studies have primarily focused on NaCl brines. Herein, we use molecular dynamics (MD) simulations to study the TSSE desalination of four different brines, namely, KCl, KBr, NaCl, and NaBr using diisopropylamine as the solvent. Based on both bulk and interfacial brine-diisopropylamine MD results, here we investigate the qualitative and quantitative performance of the simulations by benchmarking these results against our experimental evaluations of these same systems. MD results provide satisfactory qualitative agreement with the experimental data of water solubilization in the organic phase and amine solubilization in the aqueous phase for the KBr, KCl, and NaBr brines. Also, the molecular mechanism of solvation of ionic species by water molecules over diisopropylamine suggested by the MD simulations is in agreement with our experimental data. However, larger qualitative and quantitative deviations were observed for the NaCl brines, and this is likely due to polarization and charge transfer effects, as quantified by our quantum chemical calculations.

42 ENGINEERING↗

The Modified Void Nucleation and Growth Model (MNAG) for Damage Evolution in BCC Ta

A void coalescence term was proposed as an addition to the original void nucleation and growth (NAG) model to accurately describe void evolution under dynamic loading. The new model, termed as modified void nucleation and growth model (MNAG model), incorporated analytic equations to explicitly account for the evolution of the void number density and the void volume fraction (damage) during void nucleation, growth, as well as the coalescence stage. The parameters in the MNAG model were fitted to molecular dynamics (MD) shock data for single-crystal and nanocrystalline Ta, and the corresponding nucleation, growth, and coalescence rates were extracted. The results suggested that void nucleation, growth, and coalescence rates were dependent on the orientation as well as grain size. Compared to other models, such as NAG, Cocks–Ashby, Tepla, and Tonks, which were only able to reproduce early or later stage damage evolution, the MNAG model was able to reproduce all stages associated with nucleation, growth, and coalescence. The MNAG model could provide the basis for hydrodynamic simulations to improve the fidelity of the damage nucleation and evolution in 3-D microstructures.

36 MATERIALS SCIENCE↗

Unsupervised learning of representative local atomic arrangements in molecular dynamics data

Molecular dynamics (MD) simulations present a data-mining challenge, given that they can generate a considerable amount of data but often rely on limited or biased human interpretation to examine their information content. By not asking the right questions of MD data we may miss critical information hidden within it. Here we combine dimensionality reduction (UMAP) and unsupervised hierarchical clustering (HDBSCAN) to quantitatively characterize prevalent coordination environments of chemical species within MD data. By focusing on local coordination, we significantly reduce the amount of data to be analyzed by extracting all distinct molecular formulas within a given coordination sphere. We then efficiently combine UMAP and HDBSCAN with alignment or shape-matching algorithms to partition these formulas into structural isomer families indicating their relative populations. The method was employed to reveal details of cation coordination in electrolytes based on molecular liquids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Interstitial hydrogen enhances the mobility of some grain boundaries in tungsten

Segregation of interstitials at a grain boundary (GB) is known to generally lower its mobility. This phenomenon, called 'solute-drag', has important ramifications on the process of recrystallization and microstructural evolution. Here, we present predictions from molecular dynamics (MD) simulations which demonstrate that interstitial hydrogen in tungsten can in fact increase the mobility of some GBs which exhibit shear coupling. Assuming a disconnection-based mechanism, activation energies and pre-factors for disconnection nucleation are predicted from simulations of shear-coupled motion. In GBs where enhanced mobility is predicted, interstitial H reduces both the activation energy and the pre-factor for disconnection nucleation, thus effectively increasing the mobility. For GBs with diminished mobility, MD predicts that presence of interstitial H reduces the pre-factor and, in some cases, increases the activation energy. The reduction in the activation energy inferred from MD simulations are confirmed by nudged elastic band calculations. Temperature-dependent structural transitions are observed for some GBs, and the effect of interstitial H is found to change with the changes in structure. The effect of interstitial H is predicted to be complex and highly variable, providing some plausible explanations for experimental observations on the recrystallization of tungsten in presence of H-loaded plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Unfolding bovine α-lactalbumin with T-jump: Characterizing disordered intermediates via time-resolved x-ray solution scattering and molecular dynamics simulations

The protein folding process often proceeds through partially folded transient states. Therefore, a structural understanding of these disordered states is crucial for developing mechanistic models of the folding process. Characterization of unfolded states remains challenging due to their disordered nature, and incorporating multiple methods is necessary. Combining the time-resolved x-ray solution scattering (TRXSS) signal with molecular dynamics (MD), we are able to characterize transient partially folded states of bovine α-lactalbumin, a model system widely used for investigation of molten globule states, during its unfolding triggered by a temperature jump. We track the unfolding process between 20 μs and 70 ms and demonstrate that it passes through three distinct kinetic states. The scattering signals associated with these transient species are then analyzed with TRXSS constrained MD simulations to produce protein structures that are compatible with the input signals. Without utilizing any experimentally extracted kinetic information, the constrained MD simulation successfully drove the protein to an intermediate molten globule state; signals for two later disordered states are refined to terminal unfolded states. From our examination of the structural characteristics of these disordered states, we discuss the implications disordered states have on the folding process, especially on the folding pathway. Finally, we discuss the potential applications and limitations of this method.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multi-scale computer-aided design and photo-controlled macromolecular synthesis boosting uranium harvesting from seawater

By integrating multi-scale computational simulation with photo-regulated macromolecular synthesis, this study presents a new paradigm for smart design while customizing polymeric adsorbents for uranium harvesting from seawater. A dissipative particle dynamics (DPD) approach, combined with a molecular dynamics (MD) study, is performed to simulate the conformational dynamics and adsorption process of a model uranium grabber, i.e., PAO m -b-PPEGMA n , suggesting that the maximum adsorption capacity with atomic economy can be achieved with a preferred block ratio of 0.18. The designed polymers are synthesized using the PET-RAFT polymerization in a microfluidic platform, exhibiting a record high adsorption capacity of uranium (11.4 ± 1.2 mg/g) in real seawater within 28 days. This study offers an integrated perspective to quantitatively assess adsorption phenomena of polymers, bridging metal-ligand interactions at the molecular level with their spatial conformations at the mesoscopic level. The established protocol is generally adaptable for target-oriented development of more advanced polymers for broadened applications.

97 MATHEMATICS AND COMPUTING↗

Molecular simulation using transfer-learned potentials for the disordered nanoscale structure of nitrogen-doped nanoporous carbons

Machine learning (ML)-based molecular dynamics (MD) simulations of the formation of a class of N-doped nanoporous carbons are performed to assess their disordered partially graphitized nanoscale structure. The study is motivated by the effectiveness of so-called nitrogen assembly carbons (NACs) for catalysis applications. Benchmark simulations for pure-C disordered graphitic systems reveal the importance of reliably capturing the vdW component of the potentials in order to accurately describe the tendency for layering of disordered graphene-like sheets. In our modeling, this is achieved by a transfer learning strategy incorporating features of the energetics from the optB88-vdW DFT functional into potentials initially trained with a less expensive functional, thereby providing a superior description of the pure-C systems. Generation from MD simulations of realistic partially graphitized structures is significantly more challenging for N-doped versus for pure C systems. However, such structures are achieved by a tailored MD simulation protocol mimicking the experimental synthesis process and in particular incorporating an annealing and subsequent quenching stages. Simulated PXRD patterns effectively reproduce the features of experimental observations for NACs, including the appearance of a prominent but broad (002) peak at around 25, and the development of another weaker feature associated with in-layer ordering of mixed C-N graphene-like sheets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular dynamics and experimental study on the adhesion mechanism of polyvinyl alcohol (PVA) fiber in alkali-activated slag/fly ash

This paper aims to study the adhesion mechanism of polyvinyl alcohol (PVA) fiber within alkali-activated slag/fly ash (AASF) matrix using molecular dynamics (MD) simulation in combination with systematic experimental characterization. The adhesion of PVA to C-(N-)A-S-H gel with different Ca/(Si+Al) and Al/Si ratios was modeled using MD simulation, with the related adsorption enthalpy calculated and the adhesion mechanism explored. The experimentally attained chemical bonding energy of PVA fiber in AASF coincides well with the simulation results. In both cases, the adhesion enhances primarily with increasing Ca/(Si+Al) ratio of C-(N-)A-S-H gel. Additionally, MD simulation indicates preferential element distributions of Ca around PVA molecule, which was confirmed experimentally by the detection of the Ca-rich C-(N-)A-S-H gel in the interfacial transition zone (ITZ). }This study provides further insights into the adhesion mechanism of PVA fiber to C-(N-)A-S-H gel formed in AASF, which is particularly valuable for the future development of PVA-based high-performance alkali-activated composites.

36 MATERIALS SCIENCE↗

Molecular mechanism of biased signaling at the kappa opioid receptor

The κ-opioid receptor (KOR) has emerged as an attractive drug target for pain management without addiction, and biased signaling through particular pathways of KOR may be key to maintaining this benefit while minimizing side-effect liabilities. As for most G protein-coupled receptors (GPCRs), however, the molecular mechanisms of ligand-specific signaling at KOR have remained unclear. To better understand the molecular determinants of KOR signaling bias, we apply structure determination, atomic-level molecular dynamics (MD) simulations, and functional assays. We determine a crystal structure of KOR bound to the G protein-biased agonist nalfurafine, the first approved KOR-targeting drug. We also identify an arrestin-biased KOR agonist, WMS-X600. Using MD simulations of KOR bound to nalfurafine, WMS-X600, and a balanced agonist U50,488, we identify three active-state receptor conformations, including one that appears to favor arrestin signaling over G protein signaling and another that appears to favor G protein signaling over arrestin signaling. These results, combined with mutagenesis validation, provide a molecular explanation of how agonists achieve biased signaling at KOR.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling prebiotic chemistries with quantum accuracy at classical costs

Molecular Dynamics (MD) simulations using classical force-fields are commonly employed in numerous scientific investigations. However, many natural processes involve bond breaking and quantum forces. This complexity is compounded by the presence of multiple competing length and timescales. For example, accurately modeling the thermodynamics and dynamics of a chemical reaction requires accounting for the concerted movements of numerous solvent molecules and ions with their own fast or slow timescales. While widely used static Density Functional Theory (DFT) calculations at 0 temperature can be beneficial for such investigations, they do not account for dynamics, and lack precision in describing the molecular environments. They particularly fail at correct, rigorous treatments of finite-temperature fluctuations, and thus generalization to experimentally relevant conditions. In PNAS Benayad et al develop a scalable, generalizable approach for designing Neural Network Potentials (NNPs) that can handle chemical reactivity in solvated systems with quantum accuracy at classical costs. Specifically, they study phosphoester bond formation and rupture, which is fundamentally relevant to the Phosphorus-Oxygen bond formation central to life, and especially for the RNA world hypothesis. The framework developed here has the potential to generalize to different chemical reactions of energy and biological relevance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Simulation and analysis of slip flow of water at hydrophobic silica surfaces of nanometer slit pores

Water flow in nanopores is controlled fundamentally by pore wettability and interfacial water features. In the research herein reported, Molecular dynamics (MD) was used to simulate water flow in nanometer slit pores of silica surfaces with variable wetting characteristics. Compared to Couette flow, the simulated slit-pores of the talc (001) and octadecyltrichlorosilane (OTS) monolayer surfaces exhibited water flow enhancement and a positive slip length at the interface, whereas water flow velocity at the quartz (001) and amorphous silica surfaces was zero, adhering to the no slip condition. More intensive interactions between the interfacial water and hydrophilic silica surfaces were confirmed by MD simulation and sum-frequency vibrational spectroscopy (SFVS) results. A water exclusion zone of approximately 3 Å was found at the hydrophobic silica surfaces by quantitative MD interfacial water analysis and validated by SFVS. This exclusion zone dimension was similar in magnitude to the slip length (4–5 Å) as determined from simulated water flow in hydrophobic silica slit pores. The simulated slip lengths at the hydrophobic surfaces (0.2–1 nm) were significantly less than the experimental slip lengths (>40 nm) reported in the literature. In the case of the experimental results, this difference appears to be due to nanobubbles expected to be present at hydrophobic surfaces.

42 ENGINEERING↗

Enhanced mobility of dislocation network nodes and its effect on dislocation multiplication and strain hardening

Understanding plastic deformation of crystals in terms of the fundamental physics of dislocations has remained a grand challenge in materials science for decades. To overcome this, the Discrete Dislocation Dynamics (DDD) method has been developed, but its lack of atomistic resolution leaves open the possibility that certain key mechanisms may be overlooked. Here, by comparing large-scale Molecular Dynamics (MD) with DDD simulations performed under identical conditions we uncover significant discrepancies in the predicted strength and microstructure evolution in BCC crystals under high-strain rate conditions. These are traced to unexpected behaviors of dislocation network nodes forming at dislocation intersections, that can move in ways not previously anticipated as revealed by MD. Once these newfound freedoms of nodal motion are incorporated, DDD simulations begin to closely match plastic evolution observed in MD. This additional mechanism of motion whereby non-screw dislocations can change their glide plane profoundly affects fundamental processes of dislocation multiplication, recovery and storage that define strength of metals.

36 MATERIALS SCIENCE↗

Accelerating amorphous polymer electrolyte screening by learning to reduce errors in molecular dynamics simulated properties

Polymer electrolytes are promising candidates for the next generation lithium-ion battery technology. Large scale screening of polymer electrolytes is hindered by the significant cost of molecular dynamics (MD) simulation in amorphous systems: the amorphous structure of polymers requires multiple, repeated sampling to reduce noise and the slow relaxation requires long simulation time for convergence. Here, we accelerate the screening with a multi-task graph neural network that learns from a large amount of noisy, unconverged, short MD data and a small number of converged, long MD data. We achieve accurate predictions of 4 different converged properties and screen a space of 6247 polymers that is orders of magnitude larger than previous computational studies. Further, we extract several design principles for polymer electrolytes and provide an open dataset for the community. Our approach could be applicable to a broad class of material discovery problems that involve the simulation of complex, amorphous materials.

36 MATERIALS SCIENCE↗

Mechanisms and stability of Li dynamics in amorphous Li-Ti-P-S-based mixed ionic–electronic conductors: A machine learning molecular dynamics study

Mixed ionic–electronic conductors (MIECs) exhibit both high ionic and electronic conductivity to improve the battery performance. In this work, we investigate the mechanism and stability of transport channels in our recently developed MIEC material, amorphous Ti-doped lithium phosphorus sulfide (LPS), using molecular dynamics (MD) simulations with a 99% accurate machine-learning force field (MLFF) trained on ab initio MD data. The achieved MLFF helps efficient large-scale MD simulations on LPS with three Ti concentrations (10%, 20%, and 30%) and six temperatures (25°C to 225°C) to calculate ionic conductivity, activation energy, Li-ion transport mechanism, and configurational entropy. Results show that ionic conductivities and activation energies are consistent with our recent experimental values. Moreover, Li-ion transport occurs via free-volume diffusion facilitated by the formation of disordered Li-S polyhedra. The enhanced stability of transport channels at 10% and 20% Ti doping, compared to 0% and 30%, is observed by analyzing the vibrational and configurational entropy of these disordered Li-S polyhedra. Overall, this study highlights the utility of MLFF-based large-scale MD simulations in explaining the transport mechanism and the stability of Li-ion in Ti-doped LPS electrolyte with significant computational efficiency.

And configuration entropy↗

Morphology and Dynamics in Hydroxide-Conducting Polysulfones

In alkaline zinc–manganese dioxide batteries, there is a need for selective polymeric separators that have good hydroxide ion conductivity but that prevent the transport of zincate (Zn(OH) 4 ) 2- . Here we investigate the nanoscale structure and hydroxide transport in two cationic polysulfones that are promising for these separators. We present the synthesis and characterization for a tetraethylammonium-functionalized polysulfone (TEA-PSU) and compare it to our previous work on an N-butylimidazolium-functionalized polysulfone (NBI-PSU). We perform atomistic molecular dynamics (MD) simulations of both polymers at experimentally relevant water contents. The MD simulations show that both polymers develop well phase separated nanoscale water domains that percolate through the polymer. Calculation of the total scattering intensity from the MD simulations reveal weak or nonexistent ionomer peaks at low wave vectors. The lack of an ionomer peak is due to a loss of contrast in the scattering. The small water domains in both polymers, with median diameters on the order of 0.5–0.7 nm, lead to hydroxide and water diffusion constants that are 1–2 orders of magnitude smaller than their values in bulk water. This confinement lowers the conductivity but also may explain the strong exclusion of zincate from the PSU membranes seen experimentally.

25 ENERGY STORAGE↗

Relating Geometric Nanoconfinement and Local Molecular Environment to Diffusion in Ionic Polymer Membranes

Understanding structure-diffusion relationships in ionic polymer membranes not only illuminates fundamental mechanisms for membrane transport, but also informs further membrane development. In this study, we employ NMR diffusometry and molecular dynamics (MD) simulations to investigate diffusion coefficients and activation energies of diffusion (Ea) for both a lithium-form perfluorosulfonic acid membrane and aqueous solutions of lithium triflate. NMR shows that, at high water/ion molar ratio (?), Ea for water diffusion is slightly lower in the membrane than in solution. Conversely, membrane transport exhibits much higher Ea at low hydration as compared to solutions. MD simulations of a model system consisting of carbon nanotubes with varying diameter reveal that Ea of diffusion clearly relates to both the geometric nanoconfinement of the hydrophilic pathways in the membrane as well as the local molecular environment. These results demonstrate that Ea of diffusion can serve as a revelatory tool for the study of molecular transport processes and the coupling of morphology with transport at the nanoscale. This study thus provides new insights and new experimental and computational models for understanding transport in a wide range of polymer membranes, such as those used in molecular separations applications.

Zhang, Rui↗