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At least 919 records · Page 51

Simulations of classical three-body thermalization in one dimension

One-dimensional systems, such as nanowires or electrons moving along strong magnetic field lines, have peculiar thermalization physics. The binary collision of pointlike particles, typically the dominant process for reaching thermal equilibrium in higher-dimensional systems, cannot thermalize a 1D system. We study how dilute classical 1D gases thermalize through three-body collisions. We consider a system of identical classical point particles with pairwise repulsive inverse power-law potential V ij ∝ 1/|x i –x j | n or the pairwise Lennard-Jones potential. Using Monte Carlo methods, we compute a collision kernel and use it in the Boltzmann equation to evolve a perturbed thermal state with temperature T toward equilibrium. We explain the shape of the kernel and its dependence on the system parameters. Additionally, we implement molecular dynamics simulations of a many-body gas and show agreement with the Boltzmann evolution in the low-density limit. For the inverse power-law potential, the rate of thermalization is proportional to ρ 2 ⁢T$\frac{1}{2}$ – $\frac{1}{n}$, where ρ is the number density. Furthermore, the corresponding proportionality constant decreases with increasing n.

1-dimensional systems↗

Mapping the Interfacial Chemistry and Structure of Partially Fluorinated Bottlebrush Polymers and Their Linear Analogues

Polymer interfaces are key to a range of applications including membranes for chemical separations, hydrophobic coatings, and passivating layers for antifouling. While important, challenges remain in probing the interfacial monolayer where the molecular ordering and orientation can change depending on the chemical makeup or processing conditions. In this work, we leverage surface specific vibrational sum frequency generation (SFG) and the associated dependence on molecular symmetry to elucidate the ordering and orientations of key functional groups for poly(2,2,2-trifluoroethyl methacrylate) bottlebrush polymers and their linear polymer analogues. These measurements were framed by atomistic molecular dynamic simulations to provide a complementary physical picture of the gas–polymer interface. Simulations and SFG measurements show that methacrylate backbones are buried beneath a layer of trifluoroethyl containing side groups that result in structurally similar interfaces regardless of the polymer molecular weight or architecture. The average orientational angles of the trifluoroethyl containing side groups differ depending on polymer linear and bottlebrush architectures, suggesting that the surface groups can reorient via available rotational degrees of freedom. Results show that the surfaces of the bottlebrush and linear polymer samples do not strongly depend on molecular weight or architecture. As such, one cannot rely on increasing the molecular weight or altering the architecture to tune surface properties. This insight into the polymer interfacial structure is expected to advance the design of new material interfaces with tailored chemical/functional properties.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Probing the state of hydrogen in δ − AlOOH at mantle conditions with machine learning potential

Hydrous and nominally anhydrous minerals are a fundamental class of solids of enormous significance to geophysics. They are the water carriers in the deep geological water cycle and impact structural, elastic, plastic, and thermodynamic properties and phase relations in Earth's forming aggregates (rocks). They play a critical role in the geochemical and geophysical processes that shape the planet. Their complexity has prevented predictive calculations of their properties, but progress in materials simulations ushered by machine-learning potentials is transforming this state of affairs. Here, we adopt a hybrid approach that combines deep learning potentials (DPs) with the strongly constrained and appropriately normed meta-generalized gradient approximation functional to simulate a prototypical hydrous system. We illustrate the success of this approach to simulate δ − AlOOH ( δ ) , a phase capable of transporting water down to near the core-mantle boundary of the Earth ( ∼ 2900 km depth and ∼ 135 GPa ) in subducting slabs. A high-throughput sampling of phase space using molecular dynamics simulations with DPs sheds light on the hydrogen-bond behavior and proton diffusion at geophysical conditions. These simulations provide a pathway for a deeper understanding of these crucial components that shape Earth's internal state. Published by the American Physical Society 2024

Luo, Chenxing (ORCID:0000000341166851)↗

Concentration Dependent Interfacial Chemistry of the NaOH(aq):Gibbsite Interface

Caustic conditions are often employed for dissolution of a wide variety of minerals, where ion sorption, surface diffusion, and interfacial organization impact surface reactivity. In the case of gibbsite, gamma-Al(OH)3, the chemistry at the NaOH(aq) interface is deeply intertwined with industrial processing of aluminum, including metal production and the disposition of Al-containing wastes. To date, little is known about the structure, speciation, and dynamic behavior of gibbsite interfaces (and that of many other minerals) with NaOH(aq)—particularly as a function of ionic strength. Yet concentration-dependent interfacial organization and dynamics are a critical starting point to develop a fundamental understanding of the factors that influence dissolution. This work reports equilibrium molecular dynamics simulations of the gamma-Al(OH)3:NaOH(aq) interface, revealing the sorption behavior and speciation of ions from 0.5–10 M [NaOH]. As inner-sphere complexes, Na+ primarily coordinates to the side of the gibbsite hexagonal cavities, while OH accepts hydrogen-bonding from the surface-OH groups. The mobility of inner-sphere Na+ and OH ions is significantly reduced due to a strong surface affinity in comparison to previous reports of NaCl, CaCl2, or BaCl2 electrolytes. At high [NaOH], contact ion pairing that is observed in the bulk solution is partially disrupted upon sorption to the gibbsite surface by the individual ion–surface interactions. The molecular-scale changes to surface speciation and competition between ion–surface vs. ion–ion interactions influence surface characterization of gibbsite and potential dissolution processes, providing a valuable baseline for starting conditions needed within future reactive molecular simulations.

alkaline solutions, IDREAM, gibbsite, molecular dy↗

Disentangling the effects of non-adiabatic interactions upon ion self-diffusion within warm dense hydrogen

Warm dense matter is a material state in the region of parameter space connecting condensed matter to classical plasma physics. In this intermediate regime, we investigate the significance of non-adiabatic electron-ion interactions upon ion dynamics. To disentangle non-adiabatic from adiabatic electron-ion interactions, we compare the ion self-diffusion coefficient from the non-adiabatic electron force field computational model with an adiabatic, classical molecular dynamics simulation. A classical pair potential developed through a force-matching algorithm ensures the only difference between the models is due to the electronic inertia. Here, we implement this new method to characterize non-adiabatic effects on the self-diffusion of warm dense hydrogen over a wide range of temperatures and densities. Ultimately we show that the impact of non-adiabatic effects is negligible for equilibrium ion dynamics in warm dense hydrogen.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Isotropic-to-Nematic Transition in Salt-Free Polyelectrolyte Coacervates from Coarse-Grained Simulations

Recent interest in complex coacervation between oppositely charged polyelectrolytes (PEs) has been fueled by its relevance to biology in the context of membraneless organelle formation within living cells. For PEs with limited flexibility (such as double-stranded DNA), theoretical treatments and recent experiments have reported the emergence of liquid crystalline order (LCO) within the resulting coacervate phases. In this work, we study the underlying physics of this phenomenon using coarse-grained molecular dynamics simulations of symmetric semiflexible-semiflexible and asymmetric semiflexible-flexible coacervates. By comparing coacervates with the corresponding semidilute solutions of neutral polymers, we demonstrate that the presence of Coulomb interactions in coacervates facilitates orientational ordering, in agreement with theoretical predictions. Quantitative comparisons between our simulations and theory indicate that, for asymmetric nematic coacervates, the strong orientational ordering of stiff polyanions induces a weak ordering of the flexible polycations-an effect that was not anticipated by available theoretical studies. Simulations reveal that, for nematic coacervates, the preferred orientation of the PE chains at the liquid-liquid coacervate-supernatant interface is parallel, and the alignment of semiflexible PEs is homogeneous. The results presented here provide new molecular-level insights into the intracoacervate LCO and will help motivate further experimental and theoretical activities in this area.

36 MATERIALS SCIENCE↗

Probing electrolyte–silica interactions through simulations of the infrared spectroscopy of nanoscale pores

The structural and dynamical properties of nanoconfined solutions can differ dramatically from those of the corresponding bulk systems. Understanding the changes induced by confinement is central to controlling the behavior of synthetic nanostructured materials and predicting the characteristics of biological and geochemical systems. A key outstanding issue is how the molecular-level behavior of nanoconfined electrolyte solutions is reflected in different experimental, particularly spectroscopic, measurements. This is addressed here through molecular dynamics simulations of the OH stretching infrared (IR) spectroscopy of NaCl, NaBr, and NaI solutions in isotopically dilute HOD/D 2 O confined in hydroxylated amorphous silica slit pores of width 1–6 nm and pH ~2. In addition, the water reorientation dynamics and spectral diffusion, accessible by pump–probe anisotropy and two-dimensional IR measurements, are investigated. In this work, the aim is to elucidate the effect of salt identity, confinement, and salt concentration on the vibrational spectra. It is found that the IR spectra of the electrolyte solutions are only modestly blue-shifted upon confinement in amorphous silica slit pores, with both the size of the shift and linewidth increasing with the halide size, but these effects are suppressed as the salt concentration is increased. This indicates the limitations of linear IR spectroscopy as a probe of confined water. However, the OH reorientational and spectral diffusion dynamics are significantly slowed by confinement even at the lowest concentrations. The retardation of the dynamics eases with increasing salt concentration and pore width, but it exhibits a more complex behavior as a function of halide.

Mesoporous material↗

Solvent effects on extractant conformational energetics in liquid–liquid extraction: a simulation study of molecular solvents and ionic liquids

Extractant design in liquid–liquid extraction (LLE) is a research frontier of metal ion separations that typically focuses on the direct extractant–metal interactions. However, a more detailed understanding of energetic drivers of separations beyond primary metal coordination is often lacking, including the role of solvent in the extractant phase. In this work, we propose a new mechanism for enhancing metal-complexant energetics with nanostructured solvents. Using molecular dynamics simulations with umbrella sampling, we find that the organic solvent can reshape the energetics of the extractant's intramolecular conformational landscape. Here, we calculate free energy profiles of different conformations of a representative bidentate extractant, n-octyl(phenyl)-N,N-diisobutyl carbamoyl methyl phosphinoxide (CMPO), in four different solvents: dodecane, tributyl phosphate (TBP), and dry and wet ionic liquid (IL) 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM][Tf 2 N]). By promoting reorganization of the extractant molecule into its binding conformation, our findings reveal how particular solvents can ameliorate this unfavorable step of the metal separation process. In particular, the charge alternating nanodomains formed in ILs substantially reduce the free energy penalty associated with extractant reorganization. Importantly, using alchemical free energy calculations, we find that this stabilization persists even when we explicitly include the extracted cation. These findings provide insight into the energetic drivers of metal ion separations and potentially suggest a new approach to designing effective separations using a molecular-level understanding of solvent effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

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↗

Using limited neural networks to assess relative mechanistic influence on shock heating in granular solids

The rapid compaction of granular media results in localized heating that can induce chemical reactions, phase transformations, and melting. However, there are numerous mechanisms in play that can be dependent on a variety of microstructural features. Machine learning techniques such as neural networks offer a ubiquitous method to develop models for physical processes. Limiting what kind of microstructural information is used as an input and assessing normalized changes in network error, the relative importance of different mechanisms can be inferred. Here we utilize binned, initial density information as network inputs to predict local shock heating in a granular high explosive trained from large-scale molecular dynamics simulations. In this study, the spatial extent of the density field used in the network is altered to assess the importance and relevant length scales of the physical mechanisms in play, where different microstructural features result in different predictive capabilities.

36 MATERIALS SCIENCE↗

Terraced spreading of simple liquids on solid surfaces

We have studied the spreading of liquid drops on a solid surface by molecular-dynamics simulations of coexisting three-phase Lennard-Jones systems of liquid, vapor, and solid. We consider both spherically symmetric atoms and diatomic molecules, and a range of interaction strengths. As the attraction between liquid and solid increases we observe a smooth transition in spreading regimes, from partial to complete to terraced wetting. In the terraced case, where distinct monomolecular layers spread with different velocities, the layers are ordered but not solid, with substantial molecular diffusion both within and between layers. The quantitative behavior resembles recent experimental findings, but the detailed dynamics differ. In particular, the layers exhibit an unusual spreading law, where their radii vary in time as R-squared approximately equal to log10t, which disagrees with experiments on polymeric liquids as well as recent calculations.

Yang, Ju-Xing↗

Phase-field model of deformation twin-grain boundary interactions in hexagonal systems

Here, a phase-field model for describing dynamic interactions between deformation twins and grain boundaries in a hexagonal close packed (HCP) metal is established. It is applied to simulating the coupled evolution mechanisms of grains and twins in magnesium (Mg) by probing the transmission of $\{10\bar{1}2\}$ deformation twins across grain boundaries. We analyze the effect of the strain relaxation near a grain boundary, which is related to the geometric compatibility arising from the misorientation angle between adjoining grains. Phase-field simulations demonstrate that twin transmission across a grain boundary into a neighboring grain leads to grain boundary migration towards the neighboring grain with a reduced grain boundary width. The preferred nucleation site of new twin variant in the neighboring grain is related to the elastic interaction energy distribution. These predicted transmission behaviors agree well with existing experimental observations and molecular dynamics simulations. By analyzing set of systematic phase-field simulation results, we establish a rotation-angle-related twin variant selection rule for analyzing the transmission of $\{10\bar{1}2\}$ deformation twins across grain boundaries in Mg and its alloys.

36 MATERIALS SCIENCE↗

Structural basis of agonist specificity of α 1A -adrenergic receptor

α 1 -adrenergic receptors (α 1 -ARs) play critical roles in the cardiovascular and nervous systems where they regulate blood pressure, cognition, and metabolism. However, the lack of specific agonists for all α 1 subtypes has limited our understanding of the physiological roles of different α 1 -AR subtypes, and led to the stagnancy in agonist-based drug development for these receptors. Here we report cryo-EM structures of α 1A -AR in complex with heterotrimeric G-proteins and either the endogenous common agonist epinephrine or the α 1A -AR-specific synthetic agonist A61603. These structures provide molecular insights into the mechanisms underlying the discrimination between α 1A -AR and α 1B -AR by A61603. Guided by the structures and corresponding molecular dynamics simulations, we engineer α 1A -AR mutants that are not responsive to A61603, and α 1B -AR mutants that can be potently activated by A61603. Together, these findings advance our understanding of the agonist specificity for α 1 -ARs at the molecular level, opening the possibility of rational design of subtype-specific agonists.

59 BASIC BIOLOGICAL SCIENCES↗

Atoms to fibers: Identifying novel processing methods in the synthesis of pitch-based carbon fibers

Understanding and optimizing the key mechanisms used in the synthesis of pitch-based carbon fibers (CFs) are challenging, because unlike polyacrylonitrile-based CFs, the feedstock for pitch-based CFs is chemically hetero- geneous, resulting in complex fabrication leading to inconsistency in the final properties. In this work, we use molecular dynamics simulations to explore the processing and chemical phase space through a framework of CF models to identify their effects on elastic performance. The results are in excellent agreement with experiments. We find that density, followed by alignment, and functionality of the molecular constituents dictate the CF mechanical properties more strongly than their size and shape. Last, we propose a previously unexplored fabrication route for high-modulus CFs. Unlike graphitization, this results in increased sp 3 fraction, achieved via generating high-density CFs. In addition, the high sp 3 fraction leads to the fabrication of CFs with isometric compressive and tensile moduli, enabling their potential applications for compressive loading.

01 COAL, LIGNITE, AND PEAT↗

Phase Diagram of Nuclear Pastas in Neutron Star Crusts

Two neural networks were trained to predict, respectively, the Euler characteristic and the curvature of nuclear pastas in neutron star crust conditions generated by molecular dynamics simulations of neutron star matter with 0.1 < x < 0.5, 0.040 fm−3 < ρ < 0.085 fm−3 (0.68 × 1014 g/cm3 < ρ < 1.43 × 1014 g/cm3), and 0.2 MeV < T < 4.0 MeV, where x is proton content, the density is ρ, and the temperature is T. The predictions of the two networks were combined to determine the nuclear pasta phase that is thermodynamically stable at a given x, ρ, and T, and a three-dimensional phase diagram that extrapolated slightly the regions of existing molecular dynamics data was computed. The jungle gym and anti-jungle gym structures are prevalent at high temperature and low density, while the anti-jungle gym and anti-gnocchi structures dominate at high temperature and high density. A diversity of structures exist at low temperatures and intermediate density and proton content. The trained models used in this work are open access and available at a public repository to promote comparison to pastas obtained with other models.

Muñoz, Jorge A. (ORCID:0000000294870079)↗

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↗

Ion density waves driving the formation of filamentary dust structures

The PlasmaKristall-4 (PK-4) experiment on the International Space Station allows for the study of the 3-dimensional interaction between plasma and dust particles. Previous simulations of the PK-4 environment have discovered fast moving ionization waves in the dc discharge. These ionization waves vary the plasma parameters by up to an order of magnitude, which may affect the mechanisms responsible for the self-organization of chains seen in the PK-4 experiment. Here, we adapt a molecular dynamics simulation to employ temporally varying plasma conditions in order to investigate the effect on the dust charging and electrostatic potential. In order to describe the differences between the average of the plasma conditions and the time-varying plasma condition, we present a model to reproduce the interaction that takes into account the negative potential from the dust grain and the positive potential from the ion wake.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Mechanistic Insights into Molecular Copper Hydride Catalysis: the Kinetic Stability of CuH Monomers toward Aggregation is a Critical Parameter for Catalyst Performance

The activity of molecular copper hydride (CuH) complexes towards the selective insertion of unsaturated hydrocarbons under mild conditions has contributed significantly to versatile methodologies for upgrading these feedstocks. However, these catalysts are particularly susceptible to deleterious aggregation, leading to the depletion of active CuH species. Little is known about the mechanisms of CuH aggregation, how it influences overall catalyst performance, and how it can be controlled. We address these challenges with mechanistic studies on a model reaction of unactivated alkene hydroboration catalyzed by (IPr*CPh 3 )CuH (LCuH). Here, we report a comprehensive mechanistic investigation of this system, identifying an aggregation pathway that continuously depletes catalytically active LCuH to form inactive CuH clusters during turnover. Deactivation of LCuH is controlled primarily by the competition between the kinetics of the initial LCuH dimerization step and that of alkene insertion. We therefore propose that a more comprehensive understanding of CuH catalyst performance must account for the kinetics of the initial LCuH dimerization step, revising a previously explored thermodynamic understanding of CuH aggregation, where the concentration of active species is controlled by equilibria established between CuH dimers and monomers. With a series of (NHC)CuH congeners (NHC = N-heterocyclic carbene), we demonstrate that ostensibly minor structural modifications to the ligand peripheries can drastically affect the LCuH dimerization kinetics, while maintaining reactivity towards on–cycle alkene insertion. We employed a computational approach based on molecular dynamics simulations to provide an in-depth understanding of how specific structural ligand modifications can substantially increase the kinetic stability of monomeric CuH catalysts. Our combined experimental and computational studies suggest strategies for rational ligand design that can be broadly applied to molecular catalyst systems that are susceptible to deactivation via aggregation pathways.

Ryan, David E. [Pacific Northwest National Laborat↗