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At least 775 records · Page 43

Self-Assembly of Silica Nanoparticles at Water–Hydrocarbon Interfaces: Insights from In Operando Small-Angle X-ray Scattering Measurements and Molecular Dynamics Simulations

To achieve tunable controls on the interactions of siliceous materials in subsurface environments bearing water and hydrocarbons, it is essential to determine the influence of hydrocarbon–water interfaces on the self-assembly of the silica particles. The hydrophilic silica particle have a tendency to aggregate on the water front of the interface. Self-assembly of silica nanoparticles proceeds via the migration of these nanoparticles to the water–hydrocarbon interface followed by aggregation at the interface. Fractal-like morphologies of assembled silica nanoparticles at water–hydrocarbon interfaces are observed. Rapid assembly of the hydrophilic silica nanoparticles at water–hydrocarbon interfaces corresponds to an overall reduction in the surface tension of water–toluene and water–heptane systems. These studies demonstrate the silica aggregation that is the precursor of silica polymerization, or nucleation and growth is influenced by the presence of hydrocarbons in subsurface geologic environments. These insights were derived from in operando ultrasmall and small-angle X-ray scattering (USAXS/SAXS) measurements, cryo-scanning electron microscopy (Cryo-SEM) imaging, and classical molecular dynamics simulations. As a result, these studies are intended to inform current and future efforts aimed at tuning silica reactivity in subsurface geologic environments to enhance permeability, the design and use of silica-based proppants to enhance fractures, and the development of effective strategies to control silica-based scaling behavior in subsurface reservoirs.

42 ENGINEERING↗

Realistic Ion Dynamics through Charge Renormalization in Nonaqueous Electrolytes

While many practically important electrolytes contain lithium ions, interactions of these ions are particularly difficult to probe experimentally because of their small X-ray and neutron scattering cross sections and large neutron absorption cross sections. Molecular dynamics (MD) is a powerful tool for understanding the properties of nonaqueous electrolyte solutions from the atomic level, but the accuracy of this computational method crucially depends on the physics built into the classical force field. In this study, we demonstrate that several force fields for lithium bistriflimide (LiTFSI) in acetonitrile yield a solution structure that is consistent with the neutron scattering experiments, yet these models produce dramatically different ion dynamics in solution. Such glaring discrepancies indicate that inadequate representation of long-range interactions leads to excessive ionic association and ion-pair clustering. We show that reasonable agreement with the experimental observations can be achieved by renormalization of the ion charges using a “titration” method suggested herewith. This simple modification produces realistic concentration dependencies for ionic diffusion and conductivity in <2 M solutions, without loss in quality for simulation of the structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Crystal Structure and Preparation of Li7La3Zr2O12 (LLZO) Solid-State Electrolyte and Doping Impacts on the Conductivity: An Overview

As an essential part of solid-state lithium-ion batteries, solid electrolytes are receiving increasing interest. Among all solid electrolytes, garnet-type Li7La3Zr2O12 (LLZO) has proven to be one of the most promising electrolytes because of its high ionic conductivity at room temperature, low activation energy, good chemical and electrochemical stability, and wide potential window. Since the first report of LLZO, extensive research has been done in both experimental investigations and theoretical simulations aiming to improve its performance and make LLZO a feasible solid electrolyte. These include developing different methods for the synthesis of LLZO, using different crucibles and different sintering temperatures to stabilize the crystal structure, and adopting different methods of cation doping to achieve more stable LLZO with a higher ionic conductivity and lower activation energy. It also includes intensive efforts made to reveal the mechanism of Li ion movement and understand its determination of the ionic conductivity of the material through molecular dynamic simulations. Nonetheless, more insightful study is expected in order to obtain LLZO with a higher ionic conductivity at room temperature and further improve chemical and electrochemical stability, while optimal multiple doping is thought to be a feasible and promising route. This review summarizes recent progress in the investigations of crystal structure and preparation of LLZO, and the impacts of doping on the lithium ionic conductivity of LLZO.

Raju, Md Mozammal (ORCID:0000000319040523)↗

The charge reduction rate for multiply charged polymer ions via ion–ion recombination at atmospheric pressure

The charge reduction of multiply charged macromolecular ions via recombination with small ions in the gas phase is commonly employed to modulate the charge on macromolecules prior to mass spectrometric and mobility analyses. We employ a recently developed continuum-Molecular Dynamics (MD) calculation approach to determine the recombination rate coefficient of multiply charged (1 to 7 excess positive charged) polyethylene glycol ions (mass of 4600 Da) with smaller singly charged anions, modeled as NO 2 – ions. The continuum-MD approach accounts explicitly for the influence of the background gas on the recombination process, accounts explicitly for ion translational, vibrational, and rotational motion, and enables recombination rate coefficient calculation in nitrogen near atmospheric pressure, wherein neither low pressure nor high pressure recombination theories are strictly applicable. Continuum-MD simulations yield recombination rate coefficients near 3.9 × 10 –14 m 3 s –1 for singly charged ions, increasing to 3.0 × 10 –11 m 3 s –1 for the +7 ion. Pre-existing collision rate coefficient expressions for rigid ions are found to be within a factor of 2–5 of calculations for all charge states, but their use requires knowledge of an appropriate collision distance, which is not well-defined for flexible polymer ions. Continuum-MD-inferred rate coefficients are incorporated into a model of charge reduction, and the charge state distribution versus anion concentration determined with it is compared to charge reduction measurements made via atmospheric pressure differential mobility analysis. Furthermore, good agreement is observed between simulations and experiments; although results are extremely sensitive to the recombination rate coefficients, experimental results are bound by models utilizing rates within a factor of 2 (0.5–2.0×) of the continuum-MD rates.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Biomembrane Structure and Material Properties Studied With Neutron Scattering

Cell membranes and their associated structures are dynamical supramolecular structures where different physiological processes take place. Detailed knowledge of their static and dynamic structures is therefore needed, to better understand membrane biology. The structure–function relationship is a basic tenet in biology and has been pursued using a range of different experimental approaches. In this review, we will discuss one approach, namely the use of neutron scattering techniques as applied, primarily, to model membrane systems composed of lipid bilayers. An advantage of neutron scattering, compared to other scattering techniques, is the differential sensitivity of neutrons to isotopes of hydrogen and, as a result, the relative ease of altering sample contrast by substituting protium for deuterium. This property makes neutrons an ideal probe for the study of hydrogen-rich materials, such as biomembranes. In this review article, we describe isotopic labeling studies of model and viable membranes, and discuss novel applications of neutron contrast variation in order to gain unique insights into the structure, dynamics, and molecular interactions of biological membranes. We specifically focus on how small-angle neutron scattering data is modeled using different contrast data and molecular dynamics simulations. We also briefly discuss neutron reflectometry and present a few recent advances that have taken place in neutron spin echo spectroscopy studies and the unique membrane mechanical data that can be derived from them, primarily due to new models used to fit the data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Network analysis uncovers the communication structure of SARS-CoV-2 spike protein identifying sites for immunogen design

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has triggered myriad efforts to understand the structure and dynamics of this complex pathogen. The spike glycoprotein of SARS-CoV-2 is a significant target for immunogens as it is the means by which the virus enters human cells, while simultaneously sporting mutations responsible for immune escape. These functional and escape processes are regulated by complex molecular-level interactions. Our study presents quantitative insights on domain and residue contributions to allosteric communication, immune evasion, and local- and global-level control of functions through the derivation of a weighted graph representation from all-atom MD simulations. Focusing on the ancestral form and the D614G-variant, we provide evidence of the utility of our approach by guiding the selection of a mutation that alters the spike’s stability. Taken together, the network approach serves as a valuable tool to evaluate communication “hot-spots” in proteins to guide design of stable immunogens.

60 APPLIED LIFE SCIENCES↗

Role of solvation site segmental dynamics on ion transport in ethylene-oxide based side-chain polymer electrolytes

Ion conducting capability is often imparted to polymeric materials through short polyether side-chains, and yet the impact of this graft polymer architecture on ion solvation and conduction has not been fully explored. Here, we use a combination of impedance spectroscopy, vibrational spectroscopy, and atomistic molecular dynamics (MD) to compare the conductivity, ionic interactions, and polymer dynamics in a series of graft polyether electrolytes. We find that in poly[(oligo ethylene oxide)methyl ether methacrylate] (POEM), a widely used graft polymer electrolyte, the ionic conductivity drops more than an order of magnitude as the side-chain length is decreased from nine ethylene oxide (EO) units to three. This difference in conductivity is unexplained by differences in the calorimetric glass transition temperature (T g ), which varies only slightly with side-chain length. Furthermore, through vibrational spectroscopy and MD simulations we demonstrate that both linear and graft polyethers solvate Li⁺ ions effectively and dissociate them from large counterions, irrespective of side-chain length. Li⁺ ions do, however, show preferential solvation by EO units far from the methacrylate backbone. Similarly, EO units far from the backbone show enhanced segmental dynamics, while those near the immobile methacrylate group move substantially more slowly, as quantified by bond vector autocorrelation relaxation times. This heterogeneity in both ion solvation and local segmental relaxation explains variation in ion conductivity where material-averaged properties such as T g and number of free ions fail to do so. Importantly, the ionic conductivity is dictated primarily by the segmental mobility of the EO units which form effective solvation sites, rather than system-wide dynamics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atomistic-Scale Simulations on Graphene Bending Near a Copper Surface

Molecular insights into graphene-catalyst surface interactions can provide useful information for the efficient design of copper current collectors with graphitic anode interfaces. As graphene bending can affect the local electron density, it should reflect its local reactivity as well. Using ReaxFF reactive molecular simulations, we have investigated the possible bending of graphene in vacuum and near copper surfaces. We describe the energy cost for graphene bending and the binding energy with hydrogen and copper with two different ReaxFF parameter sets, demonstrating the relevance of using the more recently developed ReaxFF parameter sets for graphene properties. Moreover, the draping angle at copper step edges obtained from our atomistic simulations is in good agreement with the draping angle determined from experimental measurements, thus validating the ReaxFF results.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effect of water models on structure and dynamics of lignin in solution

Lignin, a major biomass component, can be an excellent source for different monomers in the polymer industry. However, the complex and heterogeneous structure of lignin poses a significant challenge for designing energy-efficient processes for depolymerization. As many proposed depolymerization processes are solvothermal, it is essential to understand the structure and dynamics of lignin in solution, in particular aqueous solution. Here, we utilize molecular dynamics simulations to understand the effect of water models on the structure and dynamics of different model lignin oligomers (softwood and hardwood) as a function of temperature. We have examined three different water models: TIP3P, TIP4P/Ew, and flexible SPC/Fw. We find that the diffusion constant of lignin oligomers in an aqueous solution differs significantly depending on the water model used. The diffusion constant of lignin in the TIP3P water model is almost twice as large as that in SPC/Fw and TIP4P/Ew. The softwood and hardwood oligomers adopt an extended structure in TIP3P water compared to SPC/Fw and TIP4P/Ew. Given the different levels of sensitivity of transport and structural properties of aqueous lignin on water models, it is important to take these into account when discussing results from a specific water model.

09 BIOMASS FUELS↗

High Energy Density Physics of Inertial Confinement Fusion Ablator Materials

The historic December 5, 2022 experiment at Lawrence Livermore National Lab’s (LLNL) National Ignition Facility (NIF) reached fusion energy ignition for the first time. This is the most important scientific breakthrough of the 21st century paves the way to future clean inertial fusion energy (IFE). The diamond (high density carbon (HDC)) ablator material used in this experiment displays detrimental effects due to the development of hydrodynamic instabilities at the diamond/fuel interface under shock compression. New alternatives to diamond ablators are required to step up the energy yield in ICF experiments. The unique combination of mechanical strength (approaching that of diamond), the ability to accommodate high-Z dopants (in contrast to diamond), and the tunability of the properties (through synthesis material with varying sp 3 content) make amorphous carbon (a-C) a promising material for next-generation IFE ablative capsules. However, despite its critical importance to the IFE program, the behavior of a-C carbon at extreme temperatures and pressures remains largely unexplored. The primary goals of this project were to perform groundbreaking dynamic compression experiments and predictive simulations to uncover the fundamental high-energy-density physics of amorphous carbon. Our goals were (1) to uncover the metastability range of amorphous carbon and probe phase transitions to diamond or metastable supercooled liquid carbon; (2) to acquire high-quality equation of state (EOS) data and develop an experimentally validated EOS from machine-learning MD simulations of the complex states of carbon; and (3) to uncover the complex behavior of carbon liquid in both thermodynamically stable and metastable supercooled states by accessing large areas of carbon phase diagram with amorphous samples with variable sp 3 content. Our proposed experimental program included measurements of equation of state and diffraction measurements using the Omega EP laser at the Laboratory of Laser Energetics at the University of Rochester. The theoretical/simulation program involved the development of machine-learning models of the complex response of amorphous carbon under dynamic compression by performing molecular dynamics simulations at experimental time and length scales using leadership class DOE supercomputers. Simulations guided experiments to observe predicted phenomena and acquire critical experimental data in specific pressure-temperature domains to validate theoretical models. This research delivered fundamental properties of novel amorphous carbon IFE ablator material, including phase diagram and EOS. These results will aid in IFE target design and implosion experiments. A unique combination of predictive simulations and dynamic and static experiments provided a highly inspirational intellectual environment for graduate students and postdocs involved in this project.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Surface Segregation of Liquid Metal Plasma-Facing Component Alloys: A ReaxFF Investigation

Engineering liquid metal alloys offers a transformative pathway for plasma-facing components by enabling chemically tailored surfaces that can simultaneously optimize plasma-material interactions, reduce divertor heat flux, and enhance core plasma confinement, thereby advancing the commercial viability of nuclear fusion power plants. This study, employing an atomistic simulation approach, provides direct evidence that incorporating nonmetal surface-active agents (such as O and H, or their combination) enables strong surface segregation. This capability makes tin−aluminum (Sn−Al) and tin−lithium (Sn−Li) alloys, with suitable compositions, good candidates for PFC applications. Specifically, the presence of low-Z solutes (Li, Al) leads to preferential surface enrichment, which imparts low-Z sputtering characteristics, while the Sn solvent maintains thermophysical stability. To systematically examine this behavior, we developed a ReaxFF force field spanning the full Sn/Al/Li/O/H chemistry, validated it against formation energies and elastic constants, and applied it in reactive molecular dynamics simulations at fusion-relevant temperatures. We also introduced an overlapbased segregation index that captures interfacial compositional separation directly from atomistic density distributions. Here, this metric reveals a clear hierarchy of segregation regimes and provides a unified view across all systems studied. Together, these findings establish a mechanistic link between nonmetal chemistry and interfacial structure, providing a predictive framework for designing self-adaptive, low-sputtering liquid metal alloys for fusion applications.

Alloys↗

The Role of Dimer Formation in the Nucleation of Superlattice Transformations and Its Impact on Disorder

The formation of defect-free two-dimensional nanocrystal (NC) superstructures remains a challenge as persistent defects hinder charge delocalization and related device performance. Understanding defect formation is an important step toward developing strategies to mitigate their formation. However, specific mechanisms of defect formation are difficult to determine, as superlattice phase transformations that occur during fabrication are quite complex and there are a variety of factors influencing the disorder in the final structure. Here, we use Molecular Dynamics (MD) and electron microscopy in concert to investigate the nucleation of the epitaxial attachment of lead chalcogenide (PbX, where X = S, Se) NC assemblies. We use an updated implementation of an existing reactive force field in an MD framework to investigate how initial orientational (mis)alignment of the constituent building blocks impacts the final structure of the epitaxially connected superlattice. This Simple Molecular Reactive Force Field (SMRFF) captures both short-range covalent forces and long-range electrostatic forces and allows us to follow orientational and translational changes of NCs during superlattice transformation. Our simulations reveal how robust the oriented attachment is with regard to the initial configuration of the NCs, measuring its sensitivity to both in-plane and out-of-plane misorientation. We show that oriented attachment nucleates through the initial formation of dimers, which corroborate experimentally observed structures. We present high-resolution structural analysis of dimers at early stages of the superlattice transformation and rationalize their contribution to the formation of defects in the final superlattice. Collectively, the simulations and experiments presented in this paper provide insights into the nucleation of NC oriented attachment, the impact of the initial configuration of NCs on the structural fidelity of the final epitaxially connected superlattice, and the propensity to form commonly observed defects, such as missing bridges and atomic misalignment in the superlattice due to the formation of dimers. Here, we present potential strategies to mitigate the formation of superlattice defects.

36 MATERIALS SCIENCE↗

Dual mechanism of the OXA-23 carbapenemase inhibition by the carbapenem NA-1-157

Carbapenem-resistant Acinetobacter baumannii continues to be a leading cause of life-threatening infections that result in high mortality rates. The major cause of carbapenem resistance in this pathogen is the production of class D carbapenemases, enzymes that inactivate the last resort carbapenem antibiotics, thus significantly diminishing the available therapeutic options. In this study, we evaluated the interaction of OXA-23, the most widely disseminated class D carbapenemase in A. baumannii clinical isolates, with the atypically modified carbapenem, NA-1-157. The MICs of this compound against strains producing OXA-23 were reduced from highly resistant levels observed for the commercial carbapenems meropenem and imipenem (16–128 µg/mL) to sensitive or intermediate levels (2–4 µg/mL). Kinetic studies showed that NA-1-157 inhibits the enzyme due to a significant decrease (>2,000-fold) in the deacylation rate relative to its closest structural analog, meropenem. Structural studies and molecular dynamics simulations demonstrated that inhibition is caused by both the inability of a water molecule to get close enough to the scissile bond to perform deacylation and by partial decarboxylation of the catalytic lysine residue upon formation of the acyl-enzyme intermediate.

Acinetobacter baumannii↗

EZFF: Python library for multi-objective parameterization and uncertainty quantification of interatomic forcefields for molecular dynamics

Parameterization of interatomic forcefields is a necessary first step in performing molecular dynamics simulations. This is a non-trivial global optimization problem involving quantification of multiple empirical variables against one or more properties. We present EZFF, a lightweight Python library for parameterization of several types of interatomic forcefields implemented in several molecular dynamics engines against multiple objectives using genetic-algorithm-based global optimization methods. The EZFF scheme provides unique functionality such as the parameterization of hybrid forcefields composed of multiple forcefield interactions as well as built-in quantification of uncertainty in forcefield parameters and can be easily extended to other forcefield functional forms as well as MD engines.

97 MATHEMATICS AND COMPUTING↗

Mapping the structural–mechanical landscape of amorphous carbon with ReaxFF molecular dynamics

We use ReaxFF molecular dynamics (MD) to investigate the relationship between structural and mechanical properties in bulk and nanostructured amorphous carbon (a-C). The liquid-quench MD method is used to generate isotropic bulk samples with mass densities ranging from 0.96 to 3.29 g/cm3. Structural analysis identifies two types of structures with distinct short- and medium-range order: lower-density sp2-dominated a-C, which is characterized by a bimodal ring-size distribution, and higher-density sp3-dominated tetrahedral amorphous carbon (ta-C), exhibiting a unimodal ring-size distribution. Stress–strain MD simulations and analysis reveal how an atomistic structure impacts elastic properties and post-yield atomic rearrangements. All stretched structures demonstrate elastic isotropy and plasticity driven by a ring-size expansion mechanism reflected in changes in ring statistics. The plastic region is substantially larger in ta-C than in a-C due to the post-yield shift from sp3 to sp2 C dominant bonding. In both a-C and ta-C, ultimate failure occurs when a reactive crack, traversed by long sp chains, forms and propagates predominantly perpendicular to the direction of the applied strain. Oxygen infiltration into the fractured region significantly reduces stress resistance, primarily through the early rupture of long sp chains. MD simulations and analysis are extended to a-C slabs, a-C nanotubes, and partially a-C nanotubes. The latter nanostructure highlights the differences between the elastically isotropic a-C walls, which develop circumferential cracking, and the crystalline walls, which tear along crystallographic directions. These results provide a strong foundation for further computational characterization of a-C materials.

Dernov, A. (ORCID:0009000004220973)↗

Influence of nanoscale interfaces on the dynamic deformation and spall failure of Cu–Fe alloy microstructures

Additively manufactured immiscible Cu–Fe alloys can exhibit a distribution of nanoscale interfaces due to the distribution of nanoscale clusters in the equilibrium and metastable phases. Molecular dynamics simulations investigate the role of such interfaces on the phase stability and transformation behavior during shock compression, as well as the mechanisms of damage nucleation during spall failure. The model multiphase Cu–Fe systems studied here comprise a distribution of Fe clusters in an FCC Cu matrix, as well as Cu clusters in a BCC Fe matrix. The length scales of the nanoscale clusters determine the energetics of the interfaces that can result in FCC/BCC (equilibrium) or FCC/FCC (metastable) interfaces in the Cu system matrix, and BCC/FCC (equilibrium) or BCC/BCC (metastable) interfaces in the Fe matrix. The MD simulations demonstrate that nanoscale metastable interface microstructures can induce plastic deformation and also stabilize phases or suppress phase transformations in metastable phase clusters. In contrast, equilibrium interfaces can influence phase transformation thresholds and serve as additional void nucleation sites during failure.

36 MATERIALS SCIENCE↗

Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of V o complex

Rotary vacuolar adenosine triphosphatases (V-ATPases) drive transmembrane proton transport through a Vo proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, the dynamic mechanism of proton pumping remains elusive. Here, we determined a 2.7-Å cryo–electron microscopy (cryo-EM) structure of yeast V o proton channel in nanodisc that reveals the location of ordered water molecules along the proton path, details of specific protein-lipid interactions, and the architecture of the membrane scaffold protein. Moreover, we uncover a state of V o that shows the c-ring rotated by ~14°. Molecular dynamics simulations demonstrate that the two rotary states are in thermal equilibrium and depict how the protonation state of essential glutamic acid residues couples water-mediated proton transfer with c-ring rotation. Our cryo-EM models and simulations also rationalize a mechanism for inhibition of passive proton transport as observed for free V o that is generated as a result of V-ATPase regulation by reversible disassembly in vivo.

59 BASIC BIOLOGICAL SCIENCES↗

Water, Ion, and Proton Dynamics and Interactions in Nanoconfined Systems

The research was directed at understanding the role that nanoconfinement has on the dynamics and structure of liquids confined in nanometer size structures. Experiments were conducted using ultrafast infrared methods. The methods were two dimensional infrared (2D IR) spectroscopy and polarization pump-probe (PSPP) experiments. In addition FT-IR spectroscopy was used. To augment the experimental work, high level molecular dynamics simulations of the systems were conducted. The system used for confinement were nanoporous silica with essentially monodispersed pores. Pores of different diameters were studies, i.e., 2.5 nm to 8 nm. Water and organic liquids were investigated. The experiments were performed on a vibrational probe molecule, i.e., the CN stretch of the anion SeCN-. The 2D IR experiments measured spectral diffusion, which directly reported on the structural dynamics of the confined liquids. 2D IR was also used to perform chemical exchange measurements, which observed the formation and dissociation of molecular complexes with surface silanols. The PSPP experiments measured orientational relaxation of the probe molecule as well as it vibrational lifetime. All of the observables depended on the diameter of the pores and the type of liquid. The simulations of the observables provided detailed structural information on the structure of the confined liquids and there interactions with the surfaces. In addition to the study of the confinement in nanopores, water in hydrogels was also studied. The same experimental methods were used along with MD simulations. It was found the influence of hydrogels on water did not come from confinement of the water in the hydrogel polymer network, but rather from the interactions of the water with the individual monomers that compose the polymer. In addition, the temperature dependence of a polymer/water system was tracked from below to above the lower critical solution temperature to observe the nature of the phase separated polymer and how water responded to the phase separation.

36 MATERIALS SCIENCE↗