The role of surfactant force field on the properties of liquid/liquid interfaces
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Servis, Michael J.↗
SEARCH · Engineering Papers
Results for “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.
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A crystal plasticity model with an atomistically informed description of grain boundary sliding for improved predictions of deformation fields
Crystal plasticity (CP) is a powerful meso-scale technique for deformation modeling in polycrystalline materials. Crystal plasticity models typically do not include an explicit description of grain boundary (GB) sliding, which could lead to inaccurate predictions of strain distributions, especially in the vicinity of GBs. In the present study, a CP model is developed that includes GB sliding as an additional deformation mechanism and models the interaction between slip and GB sliding. Atomistic simulations are used to formulate the constitutive model for GB sliding and its interaction with incident slip. The deformation fields and structure of the GBs are obtained directly from experimental characterization and are faithfully reproduced as bicrystal systems for molecular dynamics simulations. The GBs are modeled as random-type (non-coincidence, asymmetrical) boundaries as observed from experimental data. The underlying atomistic-scale mechanism for pure sliding of random GBs was found to be analogous to fluid-flow. The interaction between incident slip and a sliding GB caused local increases in stress concentration, which further led to a momentary increase in the local sliding rate. The displacement profiles at the sliding GBs computed from the CP model with sliding accommodation are 38% more accurate than the baseline CP model as quantified by the mean squared error between the simulations and experiment. Here these results help improve the sophistication and accuracy of deformation modeling by including physics-based descriptions for GB sliding and its interaction with slip, eventually leading to more reliable predictions of micromechanical quantities.
36 MATERIALS SCIENCE↗
In-Situ SEM High Strain Rate Testing of Large Diameter Micropillars Followed by TEM and EBSD Postmortem Analysis
Background Dislocation dynamic simulations are intended as a tool to understand and predict the mechanical behavior of metallic materials, but its prediction has never been directly verified by experiments due to differences in specimen strain rate and size. Objective In this work, a comprehensive experimental framework is proposed to attempt direct comparison between experiments and discrete dislocation dynamics (DDD) modelling. Methods By integrating high-throughput sample fabrication and a customized testing apparatus, the sample size and strain rate typically employed in DDD simulations are explored experimentally. Constitutive properties such as stress-strain response are measured, and microstructural information is obtained from transmission electron microscopy (TEM) imaging, electron backscatter diffraction (EBSD), and TEM-based orientation mapping. Results Magnesium and copper were selected, as case studies, to demonstrate the newly developed experimental procedure. Measured stress-strain responses for Mg are consistent with those obtained with a miniaturized Hopkison bar experiments. Furthermore, by exploiting the validated workflow, the effect of strain rate on micropillar heterogeneous deformation and associated dislocation plasticity were revealed. Conclusion The work establishes a methodology for the systematic study of not only metals but also other materials and structures at the microscale and high strain rates.
42 ENGINEERING↗
Molecular simulation of glycerol-derived triether podands for lithium ion solvation
Solvate ionic liquids (ILs) are promising candidates for several applications due to their stability, high coulombic efficiency, and low volatility. In this work, we investigate the solvation of lithium-bistriflimide by different glycerol-derived triether solvents, using molecular dynamics simulations. Very strong interactions between Li + and the solvent oxygen sites are found, leading to significant conformational changes in the solvent. Here, by comparing the conformation of the neat solvents with their IL mixtures at different concentrations and temperatures, we find that the presence of Li + induces a distinct crown-like structure in the solvent molecules. The Li + cations and the surrounding solvent form a podand complex, which is stable even at elevated temperatures. These glycerol-derived solvents exhibit distinct interactions with Li + cations which may be exploited in electrolytic applications or lithium recovery processes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
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↗
From Nonclassical to Classical: Crystallization Seeds Reshape Nucleation Mechanisms
Crystalline seeds are widely employed in crystallization to accelerate nucleation and control product polymorphs; yet, their impact on nucleation mechanisms remains poorly understood. While homogeneous nucleation of crystals from solution often proceeds through nonclassical pathways involving amorphous intermediates, it is unclear how seeds that promote heterogeneous nucleation reshape these mechanisms and govern polymorph selection. Here, in this study, we provide the first direct evidence that crystalline seeds can bypass the need for amorphous intermediates as nucleation sites, converting nonclassical nucleation mechanisms into classical, monomer-by-monomer crystallization pathways. Using molecular dynamics simulations of zeolite synthesis, we uncover a complex reaction network of competing nucleation processes mediated by intermediate interfacial polymorphs. The interplay between thermodynamic stability and kinetic favorability of these interfacial polymorphs dictates nucleation outcomes, creating a dynamic balance between the interfacial polymorph stability and crystallization rates. Furthermore, we show that the synthesis environment-whether monomers or aggregates serve as reactants-profoundly impacts these pathways. At moderate supersaturation, seeds eliminate amorphous intermediates and promote classical nucleation, whereas high supersaturation or aggregate-based reactants favor nonclassical pathways, even in the presence of seeds. These findings establish a general framework for understanding how seeds govern crystallization mechanisms, with broad implications for controlling nucleation kinetics, polymorph selection, and material properties. While focused on zeolites, this work reveals insights that may be applicable to biominerals, pharmaceuticals, functional materials, and catalysts, providing a basis for engineering crystallization pathways in diverse applications.
Chu-Jon, Carlos [Univ. of Utah, Salt Lake City, UT↗
Liquid-Vapor Coexistence and Critical Point of Mg 2 SiO 4 From Ab Initio Simulations
Hypervelocity impact-driven vaporization is characteristic of late-stage planet formation. Yet the behavior and properties of liquid-vapor mixtures of planetary materials of interest are typically unknown. Multiphase equations of state used in hydrodynamic simulations of planet impacts therefore lack reliable data for this important phenomenon. Here, we present the first constraints on the liquid-vapor critical point and coexistence phase boundary of Mg2SiO4 computed from ab initio molecular dynamics simulations. We found that the vapor is depleted in magnesium and enriched in silica and oxygen, while the coexisting liquid is enriched in magnesium and depleted in oxygen, from which we infer vaporization is incongruent. The critical point was estimated from an equation of state fit to the data. The results are in line with recent calculations of MgSiO3 and together confirm that extant multiphase equation of state (EOS) models used in planetary accretion modeling significantly underestimate the amount of supercritical material postimpact.
58 GEOSCIENCES↗
Structural origin of disorder-induced ion conduction in NaFePO 4 cathode materials
Diffusion in NaFePO 4 can be enhanced through amorphization. Based on computations using DFT and machine learning potentials, we ascribe this phenomenon to the formation of less constrained Na-ion environments upon disordering. Most modern battery technologies depend on solid-state crystalline cathode materials. However, some of these materials are constrained by the low ionic conductivity of their most stable phases. An example of this is maricite (NaFePO 4 ). Interestingly, experiments have shown that maricite can improve its rate capability through disordering (amorphization). However, experimental characterization of amorphous cathode materials remains a major challenge, hindering a clear understanding of the structural origin of the disorder-induced improvement in sodium-ion mobility. To address this, we here employ molecular dynamics simulations by first training a machine learning potential for NaFePO 4 based on the atomic cluster expansion approach and a batch active learning potential parameterization scheme. This potential is then applied to explore the structural and dynamical properties of NaFePO 4 glasses as cathode materials. Specifically, we investigate the effect of glass structure on sodium-ion diffusion, revealing the relative influences of short-range and medium-range order features. We find significant heterogeneity in sodium-ion diffusivity in the glass, with fast-conducting ions residing in less constrained atomic environments with fewer P and Fe neighbors. These more mobile ions are also surrounded by larger ring-type structures. Overall, the results and developed approach present promising avenues for developing high-performance glassy cathodes for next-generation batteries.
Christensen, Rasmus↗
Rotational memory function of SPC/E water
Memory effects are essential for the dynamics of condensed materials and are responsible for non-exponential relaxation of correlation functions of dynamic variables through the memory function. Memory functions of dipole rotations for water have never been calculated directly from molecular dynamics simulations. We present here calculations of memory functions for single-dipole rotations and for the overall dipole moment of the sample for SPC/E water. The normalized memory functions for single-particle and collective dipole dynamics turn out to be nearly identical. This result validates theories of dielectric spectroscopy in terms of single-particle time correlation functions and the connection between the collective and single-particle relaxation times through the Kirkwood factor. The dielectric function in this formalism contains no new dynamic information that does not exist in the single-dipole correlation function. A short memory time, ≲1 fs, justifies the use of the mathematics of rotational diffusion to describe the dynamics of a single molecular dipole moment in bulk water. Here, an analytical equation for the rotational memory time is derived.
Asthagiri, Dilipkumar N. [Oak Ridge National Labor↗
Dislocation dynamics in polycrystalline materials
An extension of the dislocation dynamics method to polycrystalline materials is presented with emphasis on handling interactions between dislocations and grain boundaries. The key new features of the method include: (1) a grain boundary detection algorithm, (2) new dislocation emission criteria based on power dissipation and area growth, (3) mobility of dislocations at grain boundaries, and (4) extension of topological operations e.g. mesh adaption, collision, and dissociation to handle dislocations interacting with grain boundaries. Furthermore, verification and validation examples are executed to compare our calculations with existing analytic methods, molecular dynamics simulations, and experimental observations.
36 MATERIALS SCIENCE↗
A mesoscopic digital twin that bridges length and time scales for control of additively manufactured metal microstructures
We present our recent development of an integrated mesoscale digital twin (DT) framework for relating processing conditions, microstructures, and mechanical responses of additively manufactured (AM) metals. In particular, focusing on the laser powder bed fusion technique, we describe how individual modeling and simulation capabilities are coupled to investigate and control AM microstructural features at multiple length and time scales. We review our prior case studies that demonstrate the integrated modeling schemes, in which high-fidelity melt pool dynamics simulations provide accurate local thermal profiles and histories to subsequent AM microstructure simulations. We also report our new mechanical response modeling results for predicted AM microstructures. In addition, we illustrate how our DT framework has been validated through modeling–experiment integration, as well as how it has been practically utilized to guide and analyze AM experiments. Finally, we share our perspectives on future directions of further development of the DT framework for more efficient, accurate predictions and wider ranges of applications.
36 MATERIALS SCIENCE↗
Modeling of the amplified optical stochastic cooling experiment at IOTA
Optical Stochastic Cooling (OSC), a beam cooling technique based on Stochastic Cooling, is in the early stages of experimental development. It uses radiation produced by the beam in an undulator magnet (the pickup) to correct the momentum deviation of particles downstream in another undulator (the kicker). The OSC mechanism was recently demonstrated at Fermilab’s IOTA ring using a passive configuration. However, the cooling rate of OSC can be dramatically increased by first amplifying the undulator radiation before applying the corrective kick. In collaboration with the IOTA experiment, we developed a computational model of the OSC mechanism. This paper presents beam-dynamics simulations of the amplified-OSC configuration. We implement a model of intrabeam scattering and study the effects on beam equilibrium and diffusion rate as a function of bunch charge. Finally, we investigate the phase-space dynamics with various coupling configurations between the transverse and longitudinal planes.
43 PARTICLE ACCELERATORS↗
Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers
Hemocyanin from horseshoe crab in its active form is a homo-hexameric protein. It exists in open and closed conformations when transitioning between deoxygenated and oxygenated states. Here, we present a detailed dynamic atomistic investigation of the oxygenated and deoxygenated states of the hexameric hemocyanin using explicit solvent molecular dynamics simulations. We focus on the variation in solvent cavities and the formation of tunnels in the two conformational states. By employing principal component analysis and CVAE-based deep learning, we are able to differentiate between the dynamics of the deoxy- and oxygenated states of hemocyanin. Finally, our results identify the deoxygenated open conformation, which adopts a stable, closed conformation after the oxygenation process.
59 BASIC BIOLOGICAL SCIENCES↗
Explicit solvent machine-learned coarse-grained model of sodium polystyrene sulfonate to capture polymer structure and dynamics
In this article, strongly charged polyelectrolytes (PEs) demonstrate complex solution behavior as a function of chain length, concentrations, and ionic strength. The viscosity behavior is important to understand and is a core quantity for many applications, but aspects remain a challenge. Molecular dynamics simulations using implicit solvent coarse-grained (CG) models successfully reproduce structure, but are often inappropriate for calculating viscosities. To address the need for CG models which reproduce viscoelastic properties of one of the most studied PEs, sodium polystyrene sulfonate (NaPSS), we report our recent efforts in using Bayesian optimization to develop CG models of NaPSS which capture both polymer structure and dynamics in aqueous solutions with explicit solvent. We demonstrate that our explicit solvent CG NaPSS model with the ML-BOP water model [Chan et al. Nat Commun 10, 379 (2019)] quantitatively reproduces NaPSS chain statistics and solution structure. The new explicit solvent CG model is benchmarked against diffusivities from atomistic simulations and experimental specific viscosities for short chains. We also show that our Bayesian-optimized CG model is transferable to larger chain lengths across a range of concentrations. Overall, this work provides a machine-learned model to probe the structural, dynamic, and rheological properties of polyelectrolytes such as NaPSS and aids in the design of novel, strongly charged polymers with tunable structural and viscoelastic properties
77 NANOSCIENCE AND NANOTECHNOLOGY↗
Intercalation of Lithium into Graphite: Insights from First-Principles Simulations
Understanding ion intercalation at electrode–electrolyte interfaces is key to the development of energy storage and water desalination. Here, we investigate Li + kinetics at a prototypical interface between graphite anodes and an organic electrolyte, and we elucidate key factors that determine ion transport, using first-principles methodology coupling ab initio molecular dynamics simulations with a solvation model. We show that surface chemical composition significantly influences the kinetics of ion intercalation from the liquid into graphite. We find that this is partly related to the ion desolvation process, which varies notably for different graphite surface chemical terminations. In addition, interfacial polarization is found to play an important role in determining energy barriers for ion transfer. We also discuss the impact of electrode potentials, which is often neglected in conventional first-principles calculations despite being a key factor in device configurations. Our study provides insights into the coupling of electronic and ionic effects of interfacial chemistry on ion transport at complex electrode–electrolyte interfaces.
25 ENERGY STORAGE↗
Non-Empirical and Self-Interaction Corrections for DFTB: Towards Accurate Quantum Simulations for Large Mesoscale Systems (Final Report)
This project was comprised of two complementary (but parallel) thrusts: (1) implementing massively-parallelized computing hardware (with new computational hardware that may replace GPUs) in the density functional tight binding (DFTB) approach and (2) developing new capabilities in DFTB to calculate the electronic structure and dynamics of large chemical systems. While classical molecular dynamics can handle hundreds of thousands of atoms, it cannot provide a first-principles based description of chemical systems at the quantum level. At the other extreme, conventional Kohn-Sham DFT methods can probe the true quantum mechanical nature of chemical systems; however, these methods cannot tackle the large sizes and length scales relevant to dynamics simulations of realistic systems. The DFTB formalism utilized in this project provides a viable approach for probing these large systems at a quantum mechanical level of detail. However, to utilize the DFTB approach for accurate calculations of electronic properties, it is crucial to incorporate quantum-based corrections in DFTB since exchange-correlation effects can still remain very strong in these large systems. At the same time, enhancing the computational efficiency of DFTB is also essential since optimal computational performance is required for addressing the large size scales associated with realistic chemical systems. As such, the new non-empirical corrections and computing hardware enhancements implemented in this project will enable accurate and computationally efficient approaches to directly probe electronic properties in these large, complex systems.
36 MATERIALS SCIENCE↗
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↗
Evidence of short chains in liquid sulfur
High energy x-ray pair distribution function measurements show the average coordination number of the first shell in liquid sulfur is 1.86 ± 0.04 across the λ-transition, not precisely 2.0 as widely accepted. This indicates that upon melting, liquid sulfur does not comprise solely of S 8 rings but also possesses a significant number of short chains. Intensities of the pre-peak and first diffraction peak of the x-ray structure factor and third peak height of the pair distribution function all show deviations at the λ-transition temperature T λ , associated with the break-up of S 8 rings and the start of oligomer polymerization. A significant number of non-bonded or loosely bonded “interstitial atoms,” with an average coordination number of 0.20 ± 0.005, are also observed in the so-called “forbidden zone” between the first and second shells upon melting. The number of interstitial atoms is found to decrease to a minimum at the λ-transition, but the majority persist into the high temperature polymerized liquid. Furthermore, the existence of short chains and nearby interstitial atoms represent the two main factors required to initiate the S 8 -ring to chain transition, as proposed by recent molecular dynamics simulations.
Chemical bonding↗