Anomalous Lattice Dynamics of EuSi 2 Nanoislands: Role of Interfaces Unveiled
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Seiler, A.↗
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Spatiotemporal dynamics of ionic reorganization near biological membrane interfaces
Electrical signals in excitable cells involve spatially localized ionic fluxes through ion channels and pumps on cellular lipid membranes. Common approaches to understand how these fluxes spread assume that the membrane and the surrounding electrolyte comprise an equivalent circuit of capacitors and resistors, which ignores the localized nature of transmembrane ion transport, the resulting ionic gradients and electric fields, and their spatiotemporal relaxation. Here, we consider a model of localized ion pumping across a lipid membrane, and use theory and simulation to investigate how the electrochemical signal propagates spatiotemporally in and out of plane along the membrane. The localized pumping generates long-ranged electric fields with three distinct scaling regimes along the membrane: a constant potential near-field region, an intermediate monopolar region, and a far-field dipolar region. Upon sustained pumping, the monopolar region expands radially in plane with a steady speed that is enhanced by the dielectric mismatch and the finite thickness of the lipid membrane. For unmyelinated lipid membranes in physiological settings, we find remarkably fast propagation speeds of ∼ 40 m / s , allowing faster ionic reorganization compared to bare diffusion. Together, our paper shows that transmembrane ionic fluxes induce transient long-ranged electric fields in electrolyte solutions, which may play hitherto unappreciated roles in biological signaling. Published by the American Physical Society 2025
Row, Hyeongjoo (ORCID:000000033623512X)↗
Solvation in Space-time: Pretransition Effects in Trajectory Space
We demonstrate pretransition effects in space-time in trajectories of systems in which the dynamics displays a first-order phase transition between distinct dynamical phases. These effects are analogous to those observed for thermodynamic first-order phase transitions, most notably the hydrophobic effect in water. Considering the (infinite temperature) East model as an elementary example, we study the properties of "space-time solvation" by examining trajectories where finite space-time regions are conditioned to be inactive in an otherwise active phase. We find that solvating an inactive region of space-time within an active trajectory shows two regimes in the dynamical equivalent of solvation free energy: An "entropic" small solute regime in which uncorrelated fluctuations are sufficient to evacuate activity from the solute, and an "energetic" large solute regime which involves the formation of a solute-induced inactive domain with an associated active-inactive interface bearing a dynamical interfacial tension. We also show that as a result of this dynamical interfacial tension there is a dynamical analog of the hydrophobic collapse that drives the assembly of large hydrophobes in water. We discuss the general relevance of these results to the properties of dynamical fluctuations in systems with slow collective relaxation such as glass formers.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Amphiphilic Baskets for Supramolecular Nanoarchitectures at Interfaces: Inverted Monolayer Formation on Water
Interfacial chemistry of molecular baskets remains poorly understood despite their promise for supramolecular applications of detection and sequestration of toxic molecules including those of illicit drugs, organophosphorus compounds, and anticancer agents. We present a fundamental investigation of the interfacial behavior of three amphiphilic supramolecular baskets (ASB 4, 8, and 12), having increasingly longer yet linear alkyl chains at the top of their bowl-shaped cavity. The studies were completed at the air−water interface to elucidate surface activity, interfacial stability, self-assembly, and monolayer organization that drive inverted monolayer formation, in which the molecular arms orient toward the aqueous phase in a configuration opposite to that typically observed for lipids. Herein, surface pressure−area isotherms of ASB 4, 8, 12, deposited on a water surface, were performed in tandem with nonequilibrium relaxation experiments to quantify surface activity, thermodynamic stability, and monolayer compressibility of the baskets’ monolayer assembly. Brewster angle microscopy enabled direct visualization of morphological evolution, aggregation, and packing at the interface. We show that systematic extension of the hydrocarbon arms, from four to 12 methylene groups, progressively modifies intermolecular packing, drives distinct two-dimensional aggregation pathways, and increases number densities at the air−water interface. Atomistic molecular dynamics simulations corroborate many of these experimentally observed trends and provide mechanistic detail on the cooperative roles of basket topology and interfacial concentration in regulating the hydration structure and dynamics within the cavities generated by surface-adsorbing baskets, consistent with observed variations in surface activity and packing. Our results establish how the topology of these unique supramolecules and their concentration govern interfacial organization and offer a rational framework for designing amphiphiles with predictable behavior at soft interfaces.
Hydrocarbons↗
Influence of dynamic factors on nonwetting fluid snap-off in pores
Snap-off is an important dynamic multiphase flow phenomenon which occurs in porous media. It plays a dominant role in the residual trapping and mobilization/immobilization of nonwetting fluids such as hydrocarbons or CO 2 . Current studies, applications, and threshold criteria of snap-off are mostly based on static or equilibrium conditions. Thus, the dynamics of snap-off which is relevant for many real world applications has rarely been systematically studied. While a static criterion indicates the snap-off potential for nonwetting fluids, the competition between the time required for snap-off and the local pore throat capillary number determines whether snap-off actually occurs. Using a theoretical model to couple the wetting film thickness to the local capillary number at the pore throat, we analyzed the dynamics of the wetting/nonwetting interface instability in sinusoidally constricted capillary tubes. The influence of dynamic factors as encapsulated by the effect of local capillary number on nonwetting fluid snap-off time were investigated for varying pore throat to pore body aspect ratio and pore body distances. Finally, the analysis showed that snap-off can be inhibited by a sufficiently large local capillary number even in cases where the static snap-off criterion has been met.
58 GEOSCIENCES↗
Insights into Sorption and Molecular Transport of Aqueous Glucose into Zeolite Nanopores
Liquid-phase heterogeneous catalysis using zeolites is important for biomass conversion to fuels and chemicals. There is a substantial body of work on gas-phase sorption in zeolites with different topologies; however, studies investigating the diffusion of complex molecules in liquid medium into zeolitic nanopores are scarce. Here, we present a molecular dynamics study to understand the sorption and diffusion of aqueous β-d-glucose into β-zeolite silicate at T = 395 K and P = 1 bar. Through 2-μs-long molecular dynamics trajectories, we reveal the role of the solvent, the kinetics of the pore filling, and the effect of the water model on these properties. We find that the glucose and water loading is a function of the initial glucose concentration. Although the glucose concentration increases monotonically with the initial glucose concentration, the water loading exhibits a nonmonotonic behavior. At the highest initial concentration (~20 wt %), we find that the equilibrium loading of glucose is approximately five molecules per unit cell and displays a weak dependence on the water model. Glucose molecules follow a single-file diffusion in the nanopores due to confinement. Here, the dynamics of glucose and water molecules slows significantly at the interface. The average residence time for glucose molecules is an order of magnitude larger than that in the bulk solution, while it is about twice as large for the water molecules. Our simulations reveal critical molecular details of the glucose molecule’s local environment inside the zeolite pore relevant to catalytic conversion of biomass to valuable chemicals.
09 BIOMASS FUELS↗
Pressure dependence of Kapitza resistance at gold/water and silicon/water interfaces
We conducted non-equilibrium molecular dynamics simulations to investigate Kapitza length at solid/liquid interfaces under the effects of bulk liquid pressures. Gold and silicon were utilized as hydrophilic and hydrophobic solid walls with different wetting surface behaviors, while the number of confined liquid water molecules was adjusted to obtain different pressures inside the channels. The interactions of solid/liquid couples were reparameterized accurately by measuring the water contact angle of solid substrates. In this paper, we present a thorough analysis of the structure, normal stress, and temperature distribution of liquid water to elucidate thermal energy transport across interfaces. Our results demonstrate excellent agreement between the pressures of liquid water in nano-channels and published thermodynamics data. The pressures measured as normal stress components were characterized using a long cut-off distance reinforced by a long-range van der Waals tail correction term. To clarify the effects of bulk liquid pressures on water structure at hydrophilic and hydrophobic solid surfaces, we defined solid/liquid interface spacing as the distance between the surface and the peak value of the first water density layer. Near the gold surface, we found that interface spacing and peak value of first water density layer were constant and did not depend on bulk liquid pressure; near the silicon surface, those values depended directly upon bulk liquid. Our results reveal that the pressure dependence of Kapitza length strongly depends on the wettability of the solid surface. In the case of the hydrophilic gold surface, Kapitza length was stable despite increasing bulk liquid pressure, while it varied significantly at the hydrophobic silicon surface.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Robust Self-Healing Adhesives Based on Dynamic Urethane Exchange Reactions
Thermoset polyurethanes (PUs) have been successfully reprocessed as covalent adaptable networks (CANs) by catalyzing carbamate exchange. Here we extend bond exchange beyond the internal network cross-links to create a dynamic urethane adhesive. Interfacing PU CANs to substrates with nucleophilic functional groups creates adhesives capable of reversible transcarbamoylation with the substrate, which has not been demonstrated previously by CAN adhesives. Two types of thermoset PU films were synthesized, one containing the green carbamate exchange catalyst Zr(tmhd)4 and the other containing no catalyst. Although otherwise identical in chemical and network properties, as indicated by FT-IR spectroscopy and dynamic mechanical thermal analysis (DMTA), the film containing catalyst showed dynamic bond exchange behavior through stress relaxation analysis. When evaluated as an adhesive, the CAN film exhibited self-healing properties and retained its adhesive strength for five cycles, which is attributed to reversible covalent bonding to the glass substrate. Furthermore, this work expands industrially relevant CANs to structural adhesives and demonstrates their potential value in an application that presently employs PUs as single-use materials.
adhesive↗
The allosteric mechanism leading to an open-groove lipid conductive state of the TMEM16F scramblase
TMEM16F is a Ca 2+ -activated phospholipid scramblase in the TMEM16 family of membrane proteins. Unlike other TMEM16s exhibiting a membrane-exposed hydrophilic groove that serves as a translocation pathway for lipids, the experimentally determined structures of TMEM16F shows the groove in a closed conformation even under conditions of maximal scramblase activity. It is currently unknown if/how TMEM16F groove can open for lipid scrambling. Here we describe the analysis of ~400 µs all-atom molecular dynamics (MD) simulations of the TMEM16F revealing an allosteric mechanism leading to an open-groove, lipid scrambling competent state of the protein. The groove opens into a continuous hydrophilic conduit that is highly similar in structure to that seen in other activated scramblases. The allosteric pathway connects this opening to an observed destabilization of the Ca 2+ ion bound at the distal site near the dimer interface, to the dynamics of specific protein regions that produces the open-groove state to scramble phospholipids.
59 BASIC BIOLOGICAL SCIENCES↗
In-situ/operando X-ray absorption spectroscopic investigation of the electrode/electrolyte interface on the molecular scale
A method for performing X-ray absorption spectroscopy (XAS) in the soft X-ray region was developed to investigate the surface-sensitive electron signal of electrode/electrolyte interfaces in common multivalent based organic solvents under in situ/operando conditions. Our approach enables us to probe the molecular-scale structure of electrode interfaces by measuring total electron yield and is suitable for redox systems exhibiting low intrinsic electrochemical current. In-situ F K-edge XAS measurements in a 0.5 M Magnesium bis(trifluoromethanesulfonimide)/2-Methyltetrahydrofuran (Mg(TFSI) 2 /2-MeTHF) electrolyte were carried out to determine the evolution of interfacial species during the electrochemical charging/discharging process. Time-dependent density-functional theory (TD-DFT) simulation indicate that the F K-edge evolution is the result of interfacial chemical environment change driven by electrochemical potential. In addition, we performed the “operando XAS” which runs the CV and collects spectra simultaneously. Furthermore, by using this method, the non-equilibrium state of condensed matter interfaces and interfacial dynamical transient process can be revealed.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly
Multidrug efflux pumps of pathogenic, Gram-negative bacteria comprise an innate resistance mechanism and are key contributors to the emerging global pandemic of antibiotic resistance. Several increasingly detailed cryo-electron microscopy maps have been resolved of an entire efflux pump complex, AcrAB–TolC, resulting in atomistic structural models. Using a recent model, we have carried out nearly 40 μs of molecular dynamics simulations to study one of the key components of the protein complex AcrA, the membrane fusion protein that connects the inner-membrane-bound AcrB to the outer-membrane-bound TolC. Here, we determined a three-dimensional potential of mean force (PMF) for AcrA, which displays two main conformational basins representing assembly competent and incompetent states. Corresponding experiments show that stabilizing mutations at an interdomain interface shift the dynamic equilibrium between these states to the incompetent one, disrupting pump assembly and function and resensitizing bacteria to existing antibiotics. The modulation of AcrA dynamics through pharmacological intervention therefore presents a promising route for the development of new antibiotics.
59 BASIC BIOLOGICAL SCIENCES↗
Improving Efficiency and Stability of Perovskite Solar Cells Enabled by A Near-Infrared-Absorbing Moisture Barrier
Simultaneously improving device efficiency and stability is the most important issue in perovskite solar cell (PSC) research. Here, we strategically introduce a multi-functional interface layer (MFIL) with integrated roles of: (1) electron transport, (2) moisture barrier, (3) near-infrared photocurrent enhancement, (4) trap passivation, and (5) ion migration suppression to enhance the device performance. The narrow-band-gap non-fullerene acceptor, Y6, was screened out to replace the most commonly used PCBM in the inverted PSCs. A significantly improved power conversion efficiency of 21.0% was achieved, along with a remarkable stability (up to 1,700 h) without encapsulation under various external stimuli (light, heat, and moisture). Furthermore, systematic studies of the molecular orientation or passivation and the charge carrier dynamics at the interface between perovskite and MFIL were presented. These results offer deep insights for designing advanced interlayers and establish the correlations between molecular orientation, interface molecular bonding, trap state density, non-radiation recombination, and the device performance.
14 SOLAR ENERGY↗
Damage initiation and evolution in Al-Si layered microstructures under shock loading conditions at atomic scales
Designing materials with microstructural features like multiphase interfaces have shown significant promise for usage in the next generation defense and nuclear applications. The dynamic response of these interfaces in extreme environments is observed to vary with the deformability of individual phases, which could subsequently alter the favored damage nucleation sites related to spall failure. Here, we investigate the role of spacing of interfaces in a nanocrystalline layered Aluminum-Silicon system on the shock wave propagation behavior, and microstructural and defect evolution using classical molecular dynamics simulations. The simulations are carried out with different hypothetical Al/Si microstructures including variations in the distribution of Si grains as layers in a nanocrystalline Al matrix. The molecular dynamics simulations suggest that spall failure is preferentially initiated at Al/Si interfaces. In addition, for the same system volume and same concentration of Si, a higher number of layers is marked by an increase in shock wave velocity and reduced resistance to spall failure.
36 MATERIALS SCIENCE↗
Quantifying the Impact of Electric Fields on the Local Structure and Migration of Potassium Ions at the Orthoclase (001) Surface
Developing an understanding of the response of mineral/water interfaces to applied electric fields is central to detecting and interpreting signatures of interfacial processes in the subsurface. Here we focus density functional theory calculations on understanding K + cation binding and diffusion across the (001) surface of orthoclase feldspar under various applied electric fields with and without surface hydration. The calculations reveal how water ligands labilize surface K + cations for diffusion while also increasing their sensitivity to electric field effects on the binding energy at different surface sites. The calculations also show how the direction and strength of the electric field systematically affect surface cation mobility, sorption, and hydration behavior. Specifically, electric fields directed toward the surface increase the potassium binding energies, facilitate K + diffusion across multiple binding sites, and increase the propensity of surface K + ions to lose their hydration shells. Furthermore, the findings help fill a major knowledge gap into the impact of electric fields on mineral/water interface structure and dynamics more generally, featuring in this case a commonly found type of feldspar involved in a multitude of atmospheric and geochemical processes.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural and dynamic changes in P-Rex1 upon activation by PIP 3 and inhibition by IP 4
PIP 3 -dependent Rac exchanger 1 (P-Rex1) is abundantly expressed in neutrophils and plays central roles in chemotaxis and cancer metastasis by serving as a guanine-nucleotide exchange factor (GEF) for Rac. The enzyme is synergistically activated by PIP 3 and heterotrimeric Gβγ subunits, but mechanistic details remain poorly understood. While investigating the regulation of P-Rex1 by PIP 3 , we discovered that Ins(1,3,4,5)P 4 (IP 4 ) inhibits P-Rex1 activity and induces large decreases in backbone dynamics in diverse regions of the protein. Cryo-electron microscopy analysis of the P-Rex1·IP 4 complex revealed a conformation wherein the pleckstrin homology (PH) domain occludes the active site of the Dbl homology (DH) domain. This configuration is stabilized by interactions between the first DEP domain (DEP1) and the DH domain and between the PH domain and a 4-helix bundle (4HB) subdomain that extends from the C-terminal domain of P-Rex1. Disruption of the DH–DEP1 interface in a DH/PH-DEP1 fragment enhanced activity and led to a more extended conformation in solution, whereas mutations that constrain the occluded conformation led to decreased GEF activity. Variants of full-length P-Rex1 in which the DH–DEP1 and PH–4HB interfaces were disturbed exhibited enhanced activity during chemokineinduced cell migration, confirming that the observed structure represents the autoinhibited state in living cells. Interactions with PIP 3 -containing liposomes led to disruption of these interfaces and increased dynamics protein-wide. Our results further suggest that inositol phosphates such as IP 4 help to inhibit basal P-Rex1 activity in neutrophils, similar to their inhibitory effects on phosphatidylinositol-3-kinase.
59 BASIC BIOLOGICAL SCIENCES↗
Exchange bias training relaxation in spin glass/ferromagnet bilayers
A canonical spin glass (SG) FeAu layer is fabricated to couple to a soft ferromagnet (FM) FeNi layer. Below the SG freezing temperature, exchange bias (EB) and training are observed. Training in SG/FM bilayers is insensitive to cooling field and may suppress the EB or change the sign of the EB field from negative to positive at specific temperatures, violating from the simple power-law or the single exponential function derived from the antiferromagnet based systems. In view of the SG nature, we employ a double decay model to distinguish the contributions from the SG bulk and the SG/FM interface to training. Dynamical properties during training under different cooling fields and at different temperatures are discussed, and the nonzero shifting coefficient in the time index as a signature of slowing-down decay for SG based systems is interpreted by means of a modified Monte Carlo Metropolis algorithm.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Aqueous-Phase Acetic Acid Ketonization over Monoclinic Zirconia
The effect of aqueous phase on the acetic acid ketonization over monoclinic zirconia has been investigated using first-principles based density functional theory (DFT) calculations. To capture the aqueous phase chemistry over the solid zirconia catalyst surface, the aqueous phase is represented by 111 explicit water molecules with a liquid water density of 0.93 g/cm3 and the monoclinic zirconia is modeled by the most stable surface structure . The dynamic nature of aqueous phase/ interface was studied using ab initio molecular dynamics simulation, indicating that nearly half of the surface Zr sites are occupied by either adsorbed water molecules or hydroxyl groups at 550 K. DFT calculations show that the adsorption process of acetic acid from the liquid water phase to the surface is nearly thermodynamically neutral with a Gibbs free energy of -2.3 kJ/mol although the adsorption strength of acetic acid on the surface in aqueous phase is much stronger than in vapor phase. Therefore it is expected that the adsorption of acetic acid will dramatically affects aqueous phase ketonization reactivity over the monoclinic zirconia catalyst. Using the same ketonization mechanism via the β-keto acid intermediate, we have compared acetic acid ketonization to acetone in both vapor and aqueous phases. Our DFT calculation results show although the rate-determining step of the β-keto acid formation via the C-C coupling is not pronouncedly affected, the presence of liquid water molecules will dramatically affect dehydrogenation and hydrogenation steps via proton transfer mechanism. This work was financially supported by the United States Department of Energy (DOE)’s Bioenergy Technologies Office (BETO) and performed at the Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated for DOE by Battelle Memorial Institute. Computing time and advanced catalyst characterization use was granted by a user proposal at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL). EMSL is a national scientific user facility sponsored by the Department of Energy’s Office of Biological and Environmental Research and located at PNNL.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Assessment of a Smoothed Particle Hydrodynamics Method for Thin Film on Textured Surfaces
A large number of previous studies suggest that the behavior of the near-wall liquid micro-layer plays a key role in boiling heat transfer and boiling crisis; see examples. The thin liquid layer interacts with heater surface and 'external' two-phase flow. The net effects of these interactions define the micro-hydrodynamics that leads to dryout. As a result, a good understanding of the thin-layer hydrodynamics is significant for the accurate prediction of CHF. Recently, with the advent of nanotechnology including micro-scale manufacturing, it becomes possible to perform high heat-flux boiling experiments with controlled surface conditions. Although many reports show rich observations about the effects of surface characteristics on CHF, physical mechanisms remain not fully understood. In order to have better understanding of the above phenomena, several computational models are developed, ranging from the lubrication theory to CFD methods. The former models are limited to one-dimensional formulation and unable to deal with the dry-out phenomena. It turns out that CFD methods have a greater potential for the mechanistic study of boiling. Towards the study objective, a particle-based CFD method called Smoothed Particle Hydrodynamics (SPH) is adopted. SPH is a Lagrangian particle method for solving systems of partial differential equations. Originally SPH is proposed for fluid dynamics in the context of astrophysical problems. Because mass and density are introduced during the particle approximation, SPH is also applied in fluid dynamic problems, where mass and density are important parameters to determine, without mass loss (a limitation of interface capturing schemes in mesh-based methods). Besides, geometrically complex and/or dynamic boundaries and interfaces can be handled without undue difficulty in SPH. Currently, most SPH simulations focus on large-scale scenarios (meter scale), like flooding and solitary wave. Also some works have been done with SPH in pore-scale. As for micro- or nano-scale simulation, people usually apply Dissipative Particle Dynamics (DPD) and Molecular Dynamics (MD) for particle-based simulation. Almost no work has been done on micro-scale with SPH, so assessments are needed to investigate the capability of SPH in application of micro-hydrodynamics. The Phenomena Identification and Ranking Table (PIRT) is applied to align application's technical requirements with associated physics and materials, models, simulation code capabilities and verification, validation and uncertainty quantification activities. The figures of merit are determined as: (1) Timing of micro-layer rewetting dry surface; (2) Effects of surface features. The corresponding key phenomena are determined as: (1) Hydrodynamics; (2) Interface Dynamics; (3) Energy; (4) Surface Effect. This study deals with isothermal scenario and no energy term is considered. Based on the current needs, a new SPH package, Micro-SPH, is compiled based on SPHysics with surface tension and wettability built in. Test cases are performed with Micro-SPH to assess the capability of SPH to each phenomenon identified. NEUTRINO with incompressible SPH solver is employed to investigate micro-fluid dynamics on a surface with uniformly distributed cylindrical pillars for application purposes. (authors)
22 GENERAL STUDIES OF NUCLEAR REACTORS↗