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At least 1,279 records · Page 71

Structure Factors for Hot Neutron Matter from Ab Initio Lattice Simulations with High-Fidelity Chiral Interactions

We present the first ab initio lattice calculations of spin and density correlations in hot neutron matter using high-fidelity interactions at next-to-next-to-next-to-leading order in chiral effective field theory. These correlations have a large impact on neutrino heating and shock revival in core-collapse supernovae and are encapsulated in functions called structure factors. Unfortunately, calculations of structure factors using high-fidelity chiral interactions were well out of reach using existing computational methods. In this Letter, we solve the problem using a computational approach called the rank-one operator (RO) method. The RO method is a general technique with broad applications to simulations of fermionic many-body systems. It solves the problem of exponential scaling of computational effort when using perturbation theory for higher-body operators and higher-order corrections. Using the RO method, we compute the vector and axial static structure factors for hot neutron matter as a function of temperature and density. Here, the ab initio lattice results are in good agreement with virial expansion calculations at low densities but are more reliable at higher densities. Random phase approximation codes used to estimate neutrino opacity in core-collapse supernovae simulations can now be calibrated with ab initio lattice calculations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Thermodynamics, dynamics, and structure of supercritical water at extreme conditions

Molecular dynamics (MD) simulations to understand the thermodynamic, dynamic, and structural changes in supercritical water across the Frenkel line and the melting line have been performed. The two-phase thermodynamic model [J. Phys. Chem. B(2010), 114(24), 8191-8198] and the velocity autocorrelation functions are used to locate the Frenkel line and to calculate the thermodynamic and dynamic properties. The Frenkel lines obtained from the two-phase thermodynamic model and the velocity autocorrelation criterion do not agree with each other. Structural characteristics and the translational diffusion dynamics of water suggest that this inconsistency could arise from the two oscillatory modes in water, which are associated with the bending of hydrogen bonds and intermolecular collisions inside the first coordination shell. Finally, the overall results lead us to conclude that the universality of the Frenkel line as a dynamic crossover line from rigid to nonrigid fluids is preserved in water.

74 ATOMIC AND MOLECULAR PHYSICS↗

Adsorption of PTCDA on Si(001) − 2 × 1 surface

Adsorption structures of the 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA) molecule on the clean Si(001) − 2 × 1 surface were investigated using scanning tunneling microscopy (STM) experiments in conjunction with first principles theoretical calculations. Four dominant adsorption structures were observed in the STM experiments and their atomic coordinates on the Si(001) surface were determined by comparison between the experimental STM images and the theoretical simulations. Maximizing the number of the Si—O bonds is more crucial than that of the Si—C bonds in the PTCDA adsorption.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Potential energy surfaces for the HBr{sup +} + CO{sub 2} → Br + HOCO{sup +} reaction in the HBr{sup +} {sup 2}Π{sub 3/2} and {sup 2}Π{sub 1/2} spin-orbit states

Quantum mechanical (QM) + molecular mechanics (MM) models are developed to represent potential energy surfaces (PESs) for the HBr{sup +} + CO{sub 2} → Br + HOCO{sup +} reaction with HBr{sup +} in the {sup 2}Π{sub 3/2} and {sup 2}Π{sub 1/2} spin-orbit states. The QM component is the spin-free PES and spin-orbit coupling for each state is represented by a MM-like analytic potential fit to spin-orbit electronic structure calculations. Coupled-cluster single double and perturbative triple excitation (CCSD(T)) calculations are performed to obtain “benchmark” reaction energies without spin-orbit coupling. With zero-point energies removed, the “experimental” reaction energy is 44 ± 5 meV for HBr{sup +}({sup 2}Π{sub 3/2}) + CO{sub 2} → Br({sup 2}P{sub 3/2}) + HOCO{sup +}, while the CCSD(T) value with spin-orbit effects included is 87 meV. Electronic structure calculations were performed to determine properties of the BrHOCO{sup +} reaction intermediate and [HBr⋯OCO]{sup +} van der Waals intermediate. The results of different electronic structure methods were compared with those obtained with CCSD(T), and UMP2/cc-pVTZ/PP was found to be a practical and accurate QM method to use in QM/MM direct dynamics simulations. The spin-orbit coupling calculations show that the spin-free QM PES gives a quite good representation of the shape of the PES originated by {sup 2}Π{sub 3/2}HBr{sup +}. This is also the case for the reactant region of the PES for {sup 2}Π{sub 1/2} HBr{sup +}, but spin-orbit coupling effects are important for the exit-channel region of this PES. A MM model was developed to represent these effects, which were combined with the spin-free QM PES.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Shock–Cloud Interaction in the Solar Corona

Flare-associated coronal shock waves sometimes interact with solar prominences, leading to large-amplitude prominence oscillations (LAPOs). Such prominence activation gives us a unique opportunity to track the time evolution of shock–cloud interaction in cosmic plasmas. Although the dynamics of interstellar shock–cloud interaction has been extensively studied, coronal shock–solar prominence interaction is rarely studied in the context of shock–cloud interaction. Associated with the X5.4 class solar flare that occurred on 2012 March 7, a globally propagated coronal shock wave interacted with a polar prominence, leading to LAPO. In this paper, we studied bulk acceleration and excitation of the internal flow of the shocked prominence using three-dimensional magnetohydrodynamic (MHD) simulations. We studied eight MHD simulation runs, each with different mass density structure of the prominence, and one hydrodynamic simulation run, and we compared the result. In order to compare the observed motion of activated prominence with the corresponding simulation, we also studied prominence activation by injection of a triangular-shaped coronal shock. We found that the prominence is first accelerated mainly by magnetic tension force as well as direct transmission of the shock, and later decelerated mainly by magnetic tension force. The internal flow, on the other hand, is excited during the shock front sweeps through the prominence and damps almost exponentially. We construct a phenomenological model of bulk momentum transfer from the shock to the prominence, which agreed quantitatively with all the simulation results. Based on the phenomenological prominence activation model, we diagnosed physical parameters of the coronal shock wave. The estimated energy of the coronal shock is several percent of the total energy released during the X5.4 flare.

79 ASTRONOMY AND ASTROPHYSICS↗

Data-driven linear time advance operators for the acceleration of plasma physics simulation

In this study, we demonstrate the application of data-driven linear operator construction for time advance with a goal of accelerating plasma physics simulation. We apply dynamic mode decomposition (DMD) to data produced by the nonlinear SOLPS-ITER (Scrape-off Layer Plasma Simulator - International Thermonuclear Experimental Reactor) plasma boundary code suite in order to estimate a series of linear operators and monitor their predictive accuracy via online error analysis. We find that this approach defines when these dynamics can be represented by a sequence of approximate linear operators and is essential for providing consistent projections when compared to an unconstrained application. For linear diffusion and advection–diffusion fluid test problems, we construct and apply operators within explicit and implicit time advance schemes, demonstrating that stability can be robustly guaranteed in each case. We further investigate the use of the linear time advance operators within several integration methods including forward Euler, backward Euler, and the matrix exponential. The application of this method to simulation data from SOLPS-ITER, with varying levels of Markov chain Monte Carlo numerical noise, shows that constrained DMD operators yield a capability to identify, extract, and integrate a (slow) subset of the present timescales. Example applications show that for projected speedup factors of [Formula: see text], and [Formula: see text], a mean relative error of 3%, 5%, and 8% and maximum relative error less than 20% are achievable, which appears acceptable for typical SOLPS-ITER steady-state simulations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Charge order–superfluidity transition in a two-dimensional system of hard-core bosons and emerging domain structures

We have used high-performance parallel computations by NVIDIA graphics cards applying the method of nonlinear conjugate gradients and Monte Carlo method to observe directly the developing ground state configuration of a two-dimensional hard-core boson system with decrease in temperature, and its evolution with deviation from a half-filling. This has allowed us to explore unconventional features of a charge order—superfluidity phase transition, specifically, formation of an irregular domain structure, emergence of a filamentary superfluid structure that condenses within of the charge-ordered phase domain antiphase boundaries, and formation and evolution of various topological structures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Communication: Quantitative multi-site frequency maps for amide I vibrational spectroscopy

An accurate method for predicting the amide I vibrational spectrum of a given protein structure has been sought for many years. Significant progress has been made recently by sampling structures from molecular dynamics simulations and mapping local electrostatic variables onto the frequencies of individual amide bonds. Agreement with experiment, however, has remained largely qualitative. Previously, we used dipeptide fragments and isotope-labeled constructs of the protein G mimic NuG2b as experimental standards for developing and testing amide I frequency maps. Here, we combine these datasets to test different frequency-map models and develop a novel method to produce an optimized four-site potential (4P) map based on the CHARMM27 force field. Together with a charge correction for glycine residues, the optimized map accurately describes both experimental datasets, with average frequency errors of 2–3 cm{sup −1}. This 4P map is shown to be convertible to a three-site field map which provides equivalent performance, highlighting the viability of both field- and potential-based maps for amide I spectral modeling. The use of multiple sampling points for local electrostatics is found to be essential for accurate map performance.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure and Dynamics of Polymeric Canopies in Nanoscale Ionic Materials: An Electrical Double Layer Perspective

Nanoscale ionic materials (NIMs) are an emerging class of materials consisting of charged nanoparticles and polymeric canopies attaching to them dynamically by electrostatic interactions. Using molecular simulations, we examine the structure and dynamics of the polymeric canopies in model NIMs in which the canopy thickness is much smaller than the nanoparticle diameter. Without added electrolyte ions, the charged terminal groups of polymers adsorb strongly on charged walls, thereby electrostatically “grafting” polymers to the wall. These polymers are highly stretched. They rarely desorb from the wall, but maintain modest in-plane mobility. When electrolyte ion pairs are introduced, the counterions adsorb on the wall, causing some electrostatically “grafted” polymers to desorb. The desorbed polymers, however, are less than the adsorbed counter-ions, which leads to an overscreening of wall charges. The desorbed polymers’ charged terminal groups do not distribute uniformly across the canopy but are depleted in some regions; they adopt conformation similar to those in bulk and exchange with the “grafted” polymers rapidly, hence dilating the canopy and accelerating its dynamics. We understand these results by taking the canopy as an electrical double layer, and highlight the importance of the interplay of electrostatic and entropic effects in determining its structure and dynamics.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Impact of solvent forces and broken symmetry on the assembly of designed proteins at a liquid-solid interface

The era of protein design has enabled the creation of hybrid protein-inorganic interfaces, leading to both surface-directed self-assembly of de novo protein architectures and protein-directed formation of inorganic materials. However, the resulting patterns of protein assembly are often unexpected, implying that essential interactions are not accounted for in current design platforms. Here, we use high-speed atomic force microscopy (AFM) analyzed through machine learning to follow the assembly of protein nanorods in aqueous electrolytes on two types of mica exhibiting disparate symmetry elements, which are imprinted on the overlying hydration structure. Using Monte Carlo simulations, we reproduce the observed phases and show that an observed smectic phase, previously thought to be unstable for non-interacting rods in two dimensions, emerges when crystal symmetry introduces a directional bias. The findings demonstrate the importance of incorporating solvent forces as modulated by the hydration structure inherent to interfacial systems when designing protein assemblies at liquid-crystal interfaces. Coupling physics-based simulations that can account for these factors to de novo protein design algorithms can lead to improved design platforms for bio-inspired, hybrid materials.

bioinspired materials↗

Binding Free Energy Analysis of Colicin D, E3 and E8 to Their Respective Cognate Immunity Proteins Using Computational Simulations

Colicins are antimicrobial proteins produced by bacteria for the purpose of destroying neighboring bacteria. Colicin activity is neutralized by a specific cognate immunity protein in order to protect the host. This study investigates the structural and binding mechanisms underlying the interaction of colicin-D, -E3 and -E8 to their respective immunity proteins (ImD, Im3 and Im8) using structure prediction, molecular dynamics (MD) simulations and MM-PBSA approach of free energy calculations. High-confidence colicin-immunity (Col-Im) complex structures predicted using AlphaFold2 were subjected to MD simulations of 150 ns with GROMACS and were analyzed for the binding free energy calculation using gmx_MMPBSA. Results showed that the complex of Col_E3-Im3 exhibited the most favorable binding free energy, driven by strong van der Waals and electrostatic interactions. Col_D-ImD and Col_E8-Im8 also showed the favorable binding. Electrostatics and hydrogen bonding emerged as a key factor driving binding and stability, while polar solvation acted as a destabilizing factor across all systems. These outcomes provide an understanding of the molecular mechanisms of Col-Im systems, with potential applications for developing natural antimicrobials for food safety.

Biochemistry & Molecular Biology↗

Computational tools for the simulation and analysis of spin-polarized EPR spectra

The EPR spectra of paramagnetic species induced by photoexcitation typically exhibit enhanced absorptive and emissive features resulting from sublevel populations that differ from thermal equilibrium. The populations and the resulting spin polarization of the spectra are dictated by the selectivity of the photophysical process generating the observed state. Simulation of the spin-polarized EPR spectra is crucial in the characterization of both the dynamics of formation of the photoexcited state as well as its electronic and structural properties. EasySpin, the simulation toolbox for EPR spectroscopy, now includes extended support for the simulation of the EPR spectra of spin-polarized states of arbitrary spin multiplicity and formed by a variety of different mechanisms, including photoexcited triplet states populated by intersystem crossing, charge recombination or spin polarization transfer, spin-correlated radical pairs created by photoinduced electron transfer, triplet pairs formed by singlet fission and multiplet states arising from photoexcitation in systems containing chromophores and stable radicals. In this paper, we highlight EasySpin’s capabilities for the simulation of spin-polarized EPR spectra on the basis of illustrative examples from the literature in a variety of fields ranging across chemistry, biology, material science and quantum information science.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structure and Interaction of Ionic Liquid Monolayer on Graphite from First-Principles

The ionic-liquid/graphite interface is important in understanding the behaviors of the ionic-liquid electrolyte in carbon-based supercapacitors and Li-ion batteries. A row-like cation–anion structure of the 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)amide ([BMP][TFSA]) ionic liquid (a popular choice for interfacial studies) on the graphite surface has been suggested on the basis of scanning tunneling microscopy images, but it is unclear if this structure is the most stable one. Herein, we explore alternative models of the [BMP][TFSA] monolayer on graphite basal plane with first-principles density functional theory. We find that the checkerboard type of structure is in fact more stable than the row-like structure. We further use simulated annealing based on classical molecular dynamics simulations to obtain more stable conformations of ions on the surface. Both charge-density-difference and noncovalent-interaction analyses show that the higher stability of the checkerboard structure than the row-like structure is due to the stronger anion–surface interactions in the former. Furthermore, our work therefore suggests a new structure of the [BMP][TFSA] monolayer on the graphite basal plane.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modeling non-equilibrium discharge and validating transient plasma characteristics at above-atmospheric pressure

Non-equilibrium plasma generated from positive-pulsed nanosecond electrical discharges into desiccated air is simulated in this paper using a multi-dimensional, multi-physics plasma solver. A pin-to-pin electrode configuration is used with a fixed 5.2 mm gap spacing. Peak pulse voltages range between 10.2 and 22.5 kV. Care is taken to match the exact electrode profile from the experiments, and adjust the electron collision frequency so that breakdown limits closely match those from corresponding experimental results. The optimized numerical simulations predict qualitative streamer structure that is in close agreement with experimental observations. Quantitative measurements of atomic oxygen at the anode tip and qualitative estimates of streamer gas heating are closely matched by simulations. The model results are used to provide insight into the spatial and temporal development of the transient plasma. Furthermore, the work performed in this paper delivers a numerical tool that can be extremely useful to link the post-discharge plasma properties to low-temperature plasma ignition mechanisms that are of great interest for the automotive industry.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Near- and far-field measurements of phase-ramped frequency selective surfaces at infrared wavelengths

Near- and far-field measurements of phase-ramped loop and patch structures are presented and compared to simulations. The far-field deflection measurements show that the phase-ramped structures can deflect a beam away from specular reflection, consistent with simulations. Scattering scanning near-field optical microscopy of the elements comprising the phase ramped structures reveals part of the underlying near-field phase contribution that dictates the far-field deflection, which correlates with the far-field phase behavior that was expected. These measurements provide insight into the resonances, coupling, and spatial phase variation among phase-ramped frequency selective surface (FSS) elements, which are important for the performance of FSS reflectarrays.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A Two-Fold Structural Classification Method for Determining the Accurate Ensemble of Protein Structures

Atomic-level structural characterization of flexible proteins, such as intrinsically disordered proteins and multi-domain proteins connected by flexible linkers, is challenging as they possess distinct conformations in physiological conditions. Significant efforts have been made to develop integrated approaches by combining small angle neutron/X-ray scattering experiments with molecular simulations to reveal the distinct atomic structures and the corresponding populations for these flexible proteins. One widely used method, the basis-set supported ensemble method, classifies the simulation-generated protein conformations into a set of structural basis and then derives the corresponding populations by fitting to the experimental data. This method makes an implicit assumption that protein conformations of similar structures have similar small angle scattering profiles.The present work demonstrates that, for various protein systems ranging from compact globular proteins and flexible multidomain proteins through to intrinsically disordered proteins, this method provides inaccurate assessment of the structural ensemble of the protein molecules due to the breakdown of the assumption made. To alleviate this problem, a two-fold-clustering method is developed to cluster the simulation-generated protein structures using information on both 3D structure and scattering profiles. As benchmarked by both simulation and experimental results, this new method yields much more accurate populations of structural basis of protein molecules.

59 BASIC BIOLOGICAL SCIENCES↗

ZnO($10\bar 10$) Surface Hydroxylation under Ambient Water Vapor

The interaction of water vapor with a single crystal ZnO($10\bar 10$) surface was investigated using synchrotron-based ambient pressure X-ray photoelectron spectroscopy (APXPS). Two isobaric experiments were performed at 0.3 and 0.07 Torr water vapor pressure at sample temperatures ranging from 750 to 295 K up to a maximum of 2% relative humidity (RH). Below 10–4 % RH the ZnO($10\bar 10$) interface is covered with ~0.25 monolayers of OH groups attributed to dissociation at nonstoichiometric defect sites. At ~10–4 % RH there is a sharp onset in increased surface hydroxylation attributed to reaction at stoichiometric terrace sites. The surface saturates with an OH monolayer ~0.26 nm thick and occurs in the absence of any observable molecularly bound water, suggesting the formation of a 1 × 1 dissociated monolayer structure. This is in stark contrast to ultrahigh vacuum experiments and molecular simulations that show the optimum structure is a 2 × 1 partially dissociated H2O/OH monolayer. The sharp onset to terrace site hydroxylation at ~10–4 % RH for ZnO($10\bar 10$) contrasts with APXPS observations for MgO(100) which show a sharp onset at 10–2 % RH. A surface thermodynamic analysis reveals that this shift to lower RH for ZnO($10\bar 10$) compared to MgO(100) is due to a more favorable Gibbs free energy for terrace site hydroxylation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Repetitive proteins that undergo large conformational changes evade structural prediction algorithms

Protein structure prediction algorithms, such as AlphaFold, have accelerated protein design and advanced the understanding of the relationship between amino acid sequence and protein structure. However, these algorithms are limited in their ability to predict the structures of conformationally dynamic, intrinsically disordered, and stimuli-responsive proteins. To evaluate sequence-to-structure predictions of such challenging proteins, we explored a class of conformationally dynamic, repeats-in-toxin (RTX) proteins. RTX proteins adopt intrinsically disordered conformations in the absence of calcium and undergo reversible folding into β-roll structures upon binding to calcium. RTX proteins are characterized by tandem repeats of the sequence GGXGXDXUX, in which X can be any amino acid and U is an aliphatic amino acid. We designed RTX sequence variants with global substitutions of nonconserved amino acids, tandem repeats of consensus sequences GGAGXDTLY, and tandem repeats of scrambled sequences GGAGXDTYL. AlphaFold2 and AlphaFold3 predicted that all of these RTX variants adopt β-roll structures, characteristic of wild-type RTX bound to calcium. However, modeling the predicted structures with molecular dynamics simulations and characterizing the protein variants with circular dichroism spectroscopy, small-angle x-ray scattering, and x-ray crystallography revealed that variants adopt diverse, sequence-dependent structures in the absence and presence of calcium. To better design proteins for applications in biotechnology and sustainability, it is critical to build predictive tools that consider intrinsically disordered protein states and validate these tools with multi-mode, multi-scale experimental data.

Chang, Marina P. [Stanford Univ., CA (United State↗