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At least 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Dataset for manuscript "Consequences of the failure of equipartition for the p-V behavior of liquid water and the hydration free energy components of a small protein"

Previously, we showed that in the molecular dynamics simulation of a rigid model of water it is necessary to use an integration time-step dt that is less than or equal to 0.5 fs to ensure equipartition between translational and rotational modes. We extended that study in the NVT ensemble to NpT conditions and to an aqueous protein. We study neat liquid water with the rigid, SPC/E model and the protein BBA (PDB ID: 1FME) solvated in the rigid, TIP3P model. We examined integration time-steps ranging from 0.5 fs to 4.0 fs for various thermostat plus barostat combinations. We find that a small time-step, dt, is necessary to ensure consistent prediction of the simulation volume. Hydrogen mass repartitioning alleviates the problem somewhat, but is ineffective for the typical time-step used with this approach. The compressibility, a measure of volume fluctuations, is seen to be sensitive to dt. Using the mean volume estimated from the NpT simulation, we examined the electrostatic and van der Waals contribution to the hydration free energy of the protein in the NVT ensemble. These contributions are also sensitive to dt. In going from a time-step of 2 fs to a time-step of 0.5 fs, the change in the net electrostatic plus van der Waals contribution to the hydration of BBA is already in excess of the folding free energy reported for this protein. The data-set contains the simulation metadata and log files that support the claims noted above.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Thermodynamically consistent Cahn–Hilliard–Navier–Stokes equations using the metriplectic dynamics formalism

Cahn–Hilliard–Navier–Stokes (CHNS) systems describe flows with two-phases, e.g., a liquid with bubbles. Obtaining constitutive relations for general dissipative processes for such systems, which are thermodynamically consistent, can be a challenge. We show how the metriplectic 4-bracket formalism (Morrison and Updike, 2024) achieves this in a straightforward, in fact algorithmic, manner. First, from the noncanonical Hamiltonian formulation for the ideal part of a CHNS system we obtain an appropriate Casimir to serve as the entropy in the metriplectic formalism that describes the dissipation (e.g. viscosity, heat conductivity and diffusion effects). General thermodynamics with the concentration variable and its thermodynamics conjugate, the chemical potential, are included. Having expressions for the Hamiltonian (energy), entropy, and Poisson bracket, we describe a procedure for obtaining a metriplectic 4-bracket that describes thermodynamically consistent dissipative effects. The 4-bracket formalism leads naturally to a general CHNS system that allows for anisotropic surface energy effects. Furthermore, this general CHNS system reduces to cases in the literature, to which we can compare.

Cahn–Hilliard↗
DOE OSTI2024

Biomolecular condensates form spatially inhomogeneous network fluids

The functions of biomolecular condensates are thought to be influenced by their material properties, and these will be determined by the internal organization of molecules within condensates. However, structural characterizations of condensates are challenging, and rarely reported. Here, we deploy a combination of small angle neutron scattering, fluorescence recovery after photobleaching, and coarse-grained molecular dynamics simulations to provide structural descriptions of model condensates that are formed by macromolecules from nucleolar granular components (GCs). We show that these minimal facsimiles of GCs form condensates that are network fluids featuring spatial inhomogeneities across different length scales that reflect the contributions of distinct protein and peptide domains. The network-like inhomogeneous organization is characterized by a coexistence of liquid- and gas-like macromolecular densities that engenders bimodality of internal molecular dynamics. These insights suggest that condensates formed by multivalent proteins share features with network fluids formed by systems such as patchy or hairy colloids.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Simulation of Isotopic Concentrations and Gamma Spectra from Dynamic Fission Sources

A tool was developed to rapidly generate synthetic gamma-ray spectra to evaluate safeguards material control and accounting methods for liquid-fueled molten salt reactors. Molten salt reactor operations pose unique challenges to nuclear safeguards methods and protocols compared to deployed reactors designs (e.g., light water reactors). This research evaluates the use of gamma-ray spectroscopy to monitor fission product isotopic flow through a reactor model to understand expected operations and investigate changes to the spectra with material diversion scenarios. The large design space of molten salt reactors (e.g., liquid-fueled, liquid-cooled, online separations) could potentially lead to many measurement points within the reactor system. The developed analytical tool generates and evaluates synthetic gamma-ray spectra from dynamic reactor simulations by extracting isotopic inventory to generate source terms. An implementation in the Gamma Detector Response and Analysis Software (GADRAS) Application Program Interface (API) uses the source terms, a model of the reactor component, a detector response function, and measurement plan to quickly generate and analyze spectra. Prospective measurements are then evaluated in the more accurate but slower Geant4 simulations. Utilization of the developed modeling tool and analysis of the subsequent spectra enables optimization of collimation, shielding requirements, and expected count rates that are used to determine key measurement points in the modeled reactor design.

O'Brien, Sean↗
DOE OSTI2020

Fermi-liquid theory and divergences of the two-particle irreducible vertex in the periodic Anderson lattice

Here we analyze the divergences of the irreducible vertex function in dynamical mean field theory, which may indicate either a nonphysical breakdown of the perturbation theory or a response to some physical phenomenon. To investigate this question, we construct a quasiparticle vertex from the diverging irreducible vertex functions. This vertex describes the scattering between quasiparticles and quasiholes in a Fermi liquid. We show that the quasparticle vertex does not diverge in the charge channel, wherein the irreducible vertex does diverge; and we show that the quasiparticle vertex does diverge in the spin channel, wherein the irreducible vertex does not diverge. This divergence occurs at the Mott transition, wherein the Fermi-liquid theory breaks down. Both the half filled Hubbard and Anderson lattices are investigated. In general, our results support that the divergences of the irreducible vertex function do not indicate a nonphysical failure of the perturbation theory. Instead, the divergences are the mathematical consequence of inverting a matrix (the local charge susceptibility) which accumulates increasingly negative diagonal elements as the Hubbard interaction suppresses charge fluctuations. Indeed, we find that the first divergences of the irreducible vertex in both Hubbard and Anderson lattices occurs near the maximum magnitude of the (negative) vertex-connected part of the charge susceptibility.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Nucleation, growth, and superlattice formation of nanocrystals observed in liquid cell transmission electron microscopy

This work reviews the advancements and prospects of liquid cell transmission electron microscopy (TEM) imaging and analysis methods in understanding the nucleation, growth, etching, and assembly dynamics of nanocrystals. The bonding of atoms into nanoscale crystallites produces materials with nonadditive properties unique to their size and geometry. The recent application of in situ liquid cell TEM to nanocrystal development has initiated a paradigm shift, (1) from trial-and-error synthesis to a mechanistic understanding of the “synthetic reactions” responsible for the emergence of crystallites from a disordered soup of reactive species (e.g., ions, atoms, molecules) and shape-defined growth or etching; and (2) from post-processing characterization of the nanocrystals’ superlattice assemblies to in situ imaging and mapping of the fundamental interactions and energy landscape governing their collective phase behaviors. Imaging nanocrystal formation and assembly processes on the single-particle level in solution immediately impacts many existing fields, including materials science, nanochemistry, colloidal science, biology, environmental science, electrochemistry, mineralization, soft condensed-matter physics, and device fabrication.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Role of the Solvent–Surfactant Duality of Ionic Liquids in Directing Two-Dimensional Particle Assembly

Nanoparticle self-assembly plays a key role in formation of superlattices, which exhibit remarkable physical and chemical properties. However, controlling assembly remains a challenge partly due to a lack of understanding of the assembly dynamics and the difficulty in linking interfacial solution properties to interparticle forces. In this study, using liquid-cell transmission electron microscopy, self-assembly of gold nanoparticles (NPs) into superlattices in mixtures of water and ionic liquid (IL) was visualized, revealing a dual role of the IL in the assembly process. At intermediate concentrations, the IL acts as a surfactant stabilizing the particles at a well-defined equilibrium separation corresponding to the length of hydrogen bonded IL cations adsorbed onto neighboring NPs. Analysis of the interparticle forces reveals attractive long-range interactions of a van der Waals nature. At separations of 1-3 nm, interactions are dominated by attractive ion correlation and repulsive hydration forces giving rise to an energy minimum at 1.5 nm separation. The superlattice is further stabilized by hydrogen bonding, which shifts the equilibrium interparticle distance to 1.1 nm. In contrast, at higher concentrations, IL accumulates and forms a structured network in the gap between nanoparticles, where it acts as a solvent that eliminates the repulsive barrier and thus promotes particle coalescence. This solvent-surfactant duality of IL opens new opportunities for their use in directing particle assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Large-scale molecular dynamics simulations of bubble collapse in water: Effects of system size, water model, and nitrogen

Molecular dynamics simulations in the microcanonical ensemble are performed to study the collapse of a bubble in liquid water using the single-site mW and the four-site TIP4P/2005 water models. To study system size effects, simulations for pure water systems are performed using periodically replicated simulation boxes with linear dimensions, L, ranging from 32 to 512 nm with the largest systems containing 8.7 × 10 6 and 4.5 × 10 9 molecules for the TIP4P/2005 and mW water models, respectively. The computationally more efficient mW water model allows us to reach converging behavior when the bubble dynamics results are plotted in reduced units, and the limiting behavior can be obtained through linear extrapolation in L –1 . Qualitative differences are observed between simulations with the mW and TIP4P/2005 water models, but they can be explained by the models’ differences in predicted viscosity and surface tension. Although bubble collapse occurs on time scales of only hundreds of picoseconds, the system sizes used here are sufficiently large to obtain bubble dynamics consistent with the Rayleigh–Plesset equation when using the models’ thermophysical properties as input. For the conditions explored here, extreme heating of the interfacial water molecules near the time of collapse is observed for the larger mW water systems (but the model underpredicts the viscosity), whereas heating is less pronounced for the TIP4P/2005 water systems because its larger viscosity contribution slows the collapse dynamics. The presence of nitrogen within the bubble only starts to affect bubble dynamics near the very end of the initial collapse, leading to an incomplete collapse and strong rebound for the mW water model. Although nitrogen is non-condensable at 300 K, it becomes highly compressed and reaches a liquid-like density near the collapse point. We find that the dissolution of nitrogen is much slower than the movement of the collapsing water front, and the re-expansion of the dense nitrogen droplet gives rise to bubble rebound. The incompatibility of the collapse and dissolution time scales should be considered for continuum-scale modeling of bubble dynamics. Finally, we also confirm that the diffusion coefficient for dissolved nitrogen is insensitive to pressure as the liquid transitions from a compressed to a stretched state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Transport and Energetics of Carbon Dioxide in Ionic Liquids at Aqueous Interfaces

A major hurdle in utilizing carbon dioxide (CO 2 ) lies in separating it from industrial flue gas mixtures and finding suitable storage methods that enable its application in various industries. To address this issue, we utilized a combination of molecular dynamics simulations and experiments to investigate the behavior of CO 2 in common room-temperature ionic liquids (RTIL) when in contact with aqueous interfaces. Here, our investigation of RTILs, [EMIM][TFSI] and [OMIM][TFSI], and their interaction with a pure water layer mimics the environment of a previously developed ultrathin enzymatic liquid membrane for CO 2 separation. We analyzed diffusion constants and viscosity, which reveals that CO 2 molecules exhibit faster mobility within the selected ILs compared to what would be predicted solely based on the viscosity of the liquids using the standard Einstein–Stokes relation. Moreover, we calculated the free energy of translocation for various species across the aqueous–IL interface, including CO 2 and HCO 3 – . Free energy profiles demonstrate that CO 2 exhibits a more favorable partitioning behavior in the RTILs compared to that in pure water, while a significant barrier hinders the movement of HCO 3 – from the aqueous layer. Experimental measurement of the CO 2 transport in the RTILs corroborates the model. These findings strongly suggest that hydrophobic RTILs could serve as a promising option for selectively transporting CO 2 from aqueous media and concentrating it as a preliminary step toward storage.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Tunable shear thickening, aging, and rejuvenation in suspensions of shape-memory-endowed liquid crystalline particles

The morphological features of particles, notably shape anisotropy, critically influence the rheological properties of dense suspensions, spanning both natural and engineered systems. This work explores the potential of using shape memory particles to dynamically regulate suspension fluid flow through controllable shape transformations. First, we synthesize shape-memory particles with programmable anisotropy from liquid crystal elastomers, such that the stiffness and shapes of the particles can be tuned by manipulating temperature. Our findings reveal that suspensions from such particles exhibit significant tunability in shear thickening behavior, transitioning from discontinuous shear thickening to a Newtonian-like response within a narrow temperature range of 60 ° C. This capability to modulate rheological responses in situ presents an approach for addressing processing challenges in many applications where control over flow behavior is paramount. Furthermore, we also show that suspensions composed of these anisotropic particles can undergo physical aging, and evolve into a glassy state. This state can be escaped upon activation of the shape memory effect. This reversibility underscores the potential for using such materials to engineer systems that can enter or come out of kinetic arrest by leveraging internal mechanical responses to external stimuli. The insights gained here not only broaden our understanding of the interplay between particle geometry and suspension dynamics but also pave the way for leveraging ensembles of stimuli-responsive objects to precisely control collective behaviors in many-body systems.

Science & Technology - Other Topics↗
DOE OSTI2021

Understanding Gas Absorption in Multivalent Ionic Liquids via Solute-Solvent Interaction Analyses

Solute-solvent interactions are often evaluated to understand and explain gas solubilities. This information is regularly used to interpret gas solubility and separation within ionic liquids (ILs). Here, we use several different quantum chemical and previous molecular dynamics simulation results to show that strong solute-solvent interactions neither lead to high solubility nor to high selectivity, with respect to other solutes. Instead, the solute-solvent interaction strength with different isolated IL ions is affected by the electrostatic extremes. Also, the solute-solvent interaction with different IL molecules is strongly correlated to the molecular volumes or polarizabilities (within a series of same-anion based ILs).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Experimental observation of the liquid-liquid transition in bulk supercooled water under pressure

We prepared bulk samples of supercooled liquid water under pressure by isochoric heating of high-density amorphous ice to temperatures of 205 ± 10 kelvin, using an infrared femtosecond laser. Because the sample density is preserved during the ultrafast heating, we could estimate an initial internal pressure of 2.5 to 3.5 kilobar in the high-density liquid phase. After heating, the sample expanded rapidly, and we captured the resulting decompression process with femtosecond x-ray laser pulses at different pump-probe delay times. A discontinuous structural change occurred in which low-density liquid domains appeared and grew on time scales between 20 nanoseconds to 3 microseconds, whereas crystallization occurs on time scales of 3 to 50 microseconds. The dynamics of the two processes being separated by more than one order of magnitude provides support for a liquid-liquid transition in bulk supercooled water.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2024

A Self-Healing, Flowable, Yet Solid Electrolyte Suppresses Li-Metal Morphological Instabilities

In this article, lithium metal (Li 0 ) solid-state batteries encounter implementation challenges due to dendrite formation, side reactions, and movement of the electrode–electrolyte interface in cycling. Notably, voids and cracks formed during battery fabrication/operation are hot spots for failure. Here, a self-healing, flowable yet solid electrolyte composed of mobile ceramic crystals embedded in a reconfigurable polymer network is reported. This electrolyte can auto-repair voids and cracks through a two-step self-healing process that occurs at a fast rate of 5.6 µm h -1 . A dynamical phase diagram is generated, showing the material can switch between liquid and solid forms in response to external strain rates. The flowability of the electrolyte allows it to accommodate the electrode volume change during Li 0 stripping. Simultaneously, the electrolyte maintains a solid form with high tensile strength (0.28 MPa), facilitating the regulation of mossy Li 0 deposition. The chemistries and kinetics are studied by operando synchrotron X-ray and in situ transmission electron microscopy (TEM). Solid-state NMR reveals a dual-phase ion conduction pathway and rapid Li + diffusion through the stable polymer-ceramic interphase. This designed electrolyte exhibits extended cycling life in Li 0 –Li 0 cells, reaching 12 000 h at 0.2 mA cm -2 and 5000 h at 0.5 mA cm -2 . Furthermore, owing to its high critical current density of 9 mA cm -2 , the Li 0 –LiNi 0.8 Mn 0.1 Co 0.1 O 2 (NMC811) full cell demonstrates stable cycling at 5 mA cm -2 for 1100 cycles, retaining 88% of its capacity, even under near-zero stack pressure conditions.

25 ENERGY STORAGE↗
DOE OSTI2022

Multiscale modeling and nonlinear model predictive control for flue gas desulfurization

The primary source of sulfur dioxide (SO 2 ) emissions is flue gas from fossil fuels-based power plants. SO 2 emissions are known to not only cause health issues, but also have an adverse effect on the environment in various ways. Several Flue Gas Desulfurization (FGD) technologies have been incorporated in power plants. The most popular technology is Wet FGD, where a limestone slurry is used to absorb SO 2 from the flue gas. A detailed droplet scale model describing the instantaneous and finite rate chemistry is developed. The ill-posed Differential-Algebraic Equation (DAE) droplet model is reformulated to a well-posed index-1 DAE through index reduction. The droplet model is integrated with the bulk phase by incorporating gas-liquid mass transfer, and an oxidation reactor model to simulate the dynamic operation of the counter-current spray scrubber. As a result, the model has a well-conditioned Jacobian and overcomes the modeling challenges of previous works and enables numerical solution without requiring carefully selected initialization or specialized solution procedures. The model is successfully validated using power plant measurements, and nonlinear model predictive control (NMPC) studies are demonstrated to optimize recycle stream flowrates to minimize pumping costs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Direct Extraction of Sodium Hydroxide by Calix[4]pyrrole-Based Ion-Pair Receptors

Here, described in this work, are calix[4]pyrrole-based ion-pair receptors, cis/trans-1 and cis/trans-2, designed for the extraction of sodium hydroxide. An X-ray diffraction analysis of a single crystal of the cis-1·NaOH isomer isolated from a mixture of cis/trans-1 revealed a unique dimeric supramolecular structure. An average dimer in toluene-d 8 solution was inferred on the basis of diffusion-ordered spectroscopy (DOSY). Support for the proposed stoichiometry came from density functional theory (DFT) calculations. The structural stability of the dimeric cis-1·NaOH complex in toluene solution was further confirmed by ab initio molecular dynamics (AIMD) simulation with explicit representation of solvent. Under conditions of liquid–liquid extraction (LLE), purified receptors cis- and trans-2 were both found to remove NaOH from a pH 11.01 aqueous source phase into toluene with extraction efficiencies (E%) of 50–60% when used equimolar to NaOH. However, in all cases, precipitation was observed. Complexities associated with precipitation could be avoided by immobilization of the receptors onto a chemically inert poly(styrene) resin by means of solvent impregnation. The use of solvent-impregnated resins (SIRs) eliminated precipitation in solution while retaining the extraction efficiency toward NaOH. This allowed both the pH and salinity of the alkaline source phase to be lowered.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

A Monte Carlo Approach to Approximating the Effects of Pore Geometry on the Phase Behavior of Soil Freezing

Abstract Freezing in porous media is associated with a host of dynamic phenomena that stem from the presence and mobility of premelted liquid at subzero temperatures. Accurate assessments of the progressive liquid‐ice phase transition is required for predictive models of frost damage, glacier‐till coupling, and many other cold regions processes, as well as for evaluating the capacity for water storage in near‐surface extraterrestrial environments. We use a Monte Carlo approach to sample the pore space in a synthetic 3D packing of poly‐dispersed spherical particles and evaluate local geometrical constraints that allow us to assess changes in the relative proportions of pore fluid and ice. By approximating the phase boundary geometry in fine‐grained pores while considering both the curvature of the liquid‐ice interface and wetting interactions with matrix particles, our model predicts changes in phase equilibrium in granular media over a broad temperature range, where present accounting for the colligative effects of chloride and perchlorate solutes. In addition to formulating the constitutive behavior needed to better understand properties and processes in frozen soils, our results also provide insight into other aspects of phase equilibria in porous media, including the formation of methane hydrates in permafrost and marine sediments, and the partitioning between liquid water and vapor in the vadose zone.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Real-time mass spectrometric characterization of the solid–electrolyte interphase of a lithium-ion battery

Solid-electrolyte interphase (SEI) is a key component that dictates the performance of most electrochemical devices, but the understanding of its chemistry and structure has been limited by the lack of in-situ tools. In this work, we report SEI live-formation in Li-ion battery under operando condition with liquid secondary ion mass spectrometry (SIMS), which, in combination with molecular dynamics (MD) simulation, presents the first dynamic picture with molecular-accuracy about this key component. Before any interphasial chemistry occurs during the initial charging, an electric double layer forms at the electrode-electrolyte interface via the self-assembly of solvent molecules directed by both Li+ and potential of the electrified surface. Such double layer structure predicts the eventual interphasial chemistries formed from the electrolytes, where the negatively-charged electrode surface repels salt anions from the inner-Helmholtz layer and results in an inner SEI that is thin, dense and inorganic in nature but LiF-depleted. It was this dense layer that exercises the major functions of an interphase, i.e., conducting Li+ but insulating electrons. An outer layer that is electrolyte-permeable and organic-rich appears after formation of the inner SEI. In highly-concentrated electrolyte, the presence of LiF in the inner-SEI is raised due to the high population of salt anions in the double layer. These real-time observations at nano-scale reveal in general sense how an interphase inherits chemistry from inner-Helmholtz layer structure, and establish guidelines in engineering desirable interphases for the future battery chemistries.

Zhou, Yufan↗
DOE OSTI2023

Machine learning interatomic potential for silicon-nitride (Si 3 N 4 ) by active learning

Silicon nitride (Si 3 N 4 ) is an extensively used material in the automotive, aerospace, and semiconductor industries. However, its widespread use is in contrast to the scarce availability of reliable interatomic potentials that can be employed to study various aspects of this material on an atomistic scale, particularly its amorphous phase. In this work, we developed a machine learning interatomic potential, using an efficient active learning technique, combined with the Gaussian approximation potential (GAP) method. Our strategy is based on using an inexpensive empirical potential to generate an initial dataset of atomic configurations, for which energies and forces were recalculated with density functional theory (DFT); thereafter, a GAP was trained on these data and an iterative re-training algorithm was used to improve it by learning on-the-fly. When compared to DFT, our potential yielded a mean absolute error of 8 meV/atom in energy calculations for a variety of liquid and amorphous structures and a speed-up of molecular dynamics simulations by 3–4 orders of magnitude, while achieving a first-rate agreement with experimental results. Our potential is publicly available in an open-access repository.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗