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At least 901 records · Page 50

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↗

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↗

Active region of a functionally integrated laser – modulator

A method for the functional integration of injection lasers and modulators of generated light in a single heterostructure with spatially displaced quantum wells in the conduction and valence bands, formed by the second-type heterojunctions, is proposed. The structures and energy band diagrams of the active regions of functionally integrated lasers – modulators with amplitude and frequency modulation are considered. A physical – topological model and a technique for numerical simulation of lasers – modulators is proposed. It is shown that the maximum modulation frequencies for the proposed heterostructures, in contrast to the same frequencies implemented under pump current modulation, are not limited by the duration of transients in the laser power supply circuit and the carrier lifetime in the laser active region but are determined by the photon lifetime in the cavity. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Collaborative atomic-scale design, analysis, and nanofabrication for record breaking, single-crystal Zn(x)Cd(1-x)Te solar cell arrays

Cadmium telluride (CdTe) based photovoltaics provide a viable solar energy solution because of their short payback time, low manufacturing cost, and high theoretical efficiency ~29%. However, the highest record laboratory efficiency is only 22.1% and long-term performance degradation is ~1 % per year which hinders greater economic viability. Higher open circuit voltage (Voc) and fill factor (FF) are needed to increase the efficiency of the solar cell. Cells with record energy conversion efficiencies report short current (Jsc) values close to their theoretical maximum. However, Voc and FF in these devices remain well below their anticipated optimum. These electrical parameters depend on the quality of the various layers in the solar cell. In particular they depend on the crystalline quality including the defect and impurity concentrations. Therefore understanding how defects and impurities form and evolve in the material layers is important to design devices with higher efficiency and stability. The aim of this project is to create a novel path around the fundamental barriers to achieve high open-circuit voltages (VOC ≥ 1.0 V) in CdTe/CdS solar cells. The idea of the project was to combine nanopatterned crystal growth and alloy compositional grading (with concomitant lattice parameter and energy band gap grading) to reduce the defect density and dramatically improve spatial uniformity of ZnxCd(1-x)Te/CdS cells. The lattice mismatch between ZnTe and CdS is 3.9% compared to a much larger 9.2% between CdTe and CdS. Importantly, when crystal growth is contained to the nanoscale, the strain in each layer is reduced by a factor of two due to strain partitioning and 3D strain relief mechanisms that come into play. This reduces the strain in the ZnTe from 3.9% to 1.95% which is within the range of metamorphic crystal growth. In preliminary studies, molecular dynamics simulation of ZnTe/CdS islands predicted dislocation-free material when the patterning was reduced to ~80 nm in diameter. The energy band gap of ZnxCd(1-x)Te is also graded in conjunction with alloy composition. ZnTe has an energy band gap of 2.3 eV. Finally, an added benefit of patterned growth is that it enables direct one-to-one study of the relationships between fabrication, microstructure and performance of individual crystal grains within the array. Experimental characterization techniques such as atomic probe tomography (APT) and transmission electron microscopy (TEM) have elucidated much about the microstructure of the layers. However, the techniques are destructive, costly and have limitations on the information they convey. For example, TEM gives information with atomic scale resolution but on 2-dimensional substrates. On the other hand, APT gives 3-dimensional information but is not able to resolve atomic scale structure. Alternatively, Molecular Dynamics (MD) simulations offer a solution to rapidly generate time-resolved, 3-dimensional, atomic scale structures of crystal growth. Direct MD simulations of microstructures of Cu-doped II-VI compound multilayers can impact the research on CdTe/CdS solar cells. Such MD simulations require an interatomic potential database that includes at least four elements Cu, Cd, Te, and S. The Stillinger-Weber (SW) potential is the most widely used interatomic potential for semiconductors. However, while SW potentials have been developed for Ga-In-As-Se-Te, Al-Ga-In-P-As-Sb, Cd-Te-Zn-As-Si, In-Ga-N systems, no potentials existed to simulate Cd-Zn-Hg-Se-S-Te-Cu. The goal of this effort was to fill the knowledge gap by developing a Zn-Cd-Hg-S-Se-Te-Cu SW potential database to enable MD simulations of microstructures of Cu-doped CdTe/CdS solar cells. The new potential was then applied, via MD crystal growth simulations, to study the growth mechanisms and atomic structures of the ZnTe/Cu/CdTe/CdS multilayers under various conditions. The objective of the project was to inform the solar cell community on crystal growth and defect formation at the interface between CdTe-based epilayers grown on CdS substrates. MD simulations offered a unique opportunity to analyze the 3-dimensional crystal growth evolution of Cu doped ZnxCd(1-x)TeyS(1-y) alloys with atomic scale resolution under a variety of conditions. The effect of substrate orientation and polycrystallinity on crystal growth was studied. Substrates with grain boundaries were created and the growth evolution on these substrates were analyzed. Another focus was to elucidate the effect of dopant incorporation on the nature of polycrystallinity crystal growth. Dopants available through the Stillinger-Weber potential developed in this project included Cu, Zn, S, Se, Hg and native vacancies.

14 SOLAR ENERGY↗

Tricoupled hybrid lattice Boltzmann model for nonisothermal drying of colloidal suspensions in micropore structures

A tricoupled hybrid lattice Boltzmann model (LBM) is developed to simulate colloidal liquid evaporation and colloidal particle deposition during the nonisothermal drying of colloidal suspensions in micropore structures. An entropic multiple-relaxation-time multirange pseudopotential two-phase LBM for isothermal interfacial flow is first coupled to an extended temperature equation for simulating nonisothermal liquid drying. Then the coupled model is further coupled with a modified convection diffusion equation to consider the nonisothermal drying of colloidal suspensions. Two drying examples are considered. First, drying of colloidal suspensions in a two-pillar micropore structure is simulated in two dimensions (2D), and the final configuration of colloidal particles is compared with the experimental one. Good agreement is observed. Second, at the temperature of 343.15 K ( 70°C ), drying of colloidal suspensions in a complex spiral-shaped micropore structure containing 220 pillars is simulated (also in 2D). The drying pattern follows the designed spiral shape due to capillary pumping, i.e., transport of the liquid from larger pores to smaller ones by capillary pressure difference. Because the colloidal particles are passively carried with liquid, they accumulate at the small menisci as drying proceeds. As liquid evaporates at the small menisci, colloidal particles are deposited, eventually forming solid structures between the pillars (primarily), and at the base of the pillars (secondarily). As a result, the particle deposition conforms to the spiral route. Qualitatively, the simulated liquid and particle configurations agree well with the experimental ones during the entire drying process. Quantitatively, the model demonstrates that the evaporation rate and the particle accumulation rate slowly decrease during drying, similar to what is seen in the experimental results, which is due to the reduction of the liquid-vapor interfacial area. In conclusion, the hybrid model shows the capability and accuracy for simulating nonisothermal drying of colloidal suspensions in a complex micropore structure both qualitatively and quantitatively, as it includes all the required physics and captures all the complex features observed experimentally. Such a tricoupled LBM has a high potential to become an efficient numerical tool for further investigation of real and complex engineering problems incorporating drying of colloidal suspensions in porous media.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Recent Hydrodynamic Modeling Enhancements in OpenFAST

To improve the hydrodynamic modeling capabilities of the offshore wind design and modeling tool OpenFAST, a restructuring of the HydroDyn hydrodynamics module was undertaken with several new features implemented. The generation of the wave field is now separated from HydroDyn into a new module called SeaState. Unlike previous versions of HydroDyn, which precomputed the wave kinematics at the undisplaced positions of the hydrodynamic nodes, the new SeaState module computes the complete time history of the wave field at the vertices of a user-defined wave grid. During the simulation, the wave kinematics at any point within the grid can be efficiently interpolated, allowing the strip-theory wave loads to be evaluated based on the wave kinematics at the displaced structure position. A phase correction was also implemented for the potential-flow wave-exciting loads to account for large structure displacements. Several wave-stretching methods were implemented for the strip-theory solution along with a wave-load redistribution method that ensures smooth variation of the nodal loads as the nodes of a discrete hydrodynamic mesh enter and exit the water. The load smoothing is included to avoid the excitation of unphysical high-frequency structural vibration during hydroelastic simulations. The MacCamy-Fuchs diffraction correction for the strip-theory solution and the capability to insert a constrained NewWave into extreme stochastic sea states with directional spreading were also added. The present article documents the formulations of the new improvements to HydroDyn with example applications and numerical results.

constrained wave↗

The Simons Observatory: modeling optical systematics in the Large Aperture Telescope

We present geometrical and physical optics simulation results for the Simons Observatory Large Aperture Telescope. This work was developed as part of the general design process for the telescope, allowing us to evaluate the impact of various design choices on performance metrics and potential systematic effects. The primary goal of the simulations was to evaluate the final design of the reflectors and the cold optics that are now being built. We describe nonsequential ray tracing used to inform the design of the cold optics, including absorbers internal to each optics tube. We discuss ray tracing simulations of the telescope structure that allow us to determine geometries that minimize detector loading and mitigate spurious near-field effects that have not been resolved by the internal baffling. We also describe physical optics simulations, performed over a range of frequencies and field locations, that produce estimates of monochromatic far-field beam patterns, which in turn are used to gauge general optical performance. Finally, we describe simulations that shed light on beam sidelobes from panel gap diffraction.

Gudmundsson, Jon E. (ORCID:0000000317600355)↗

The Simons Observatory: Modeling Optical Systematics in the Large Aperture Telescope

We present geometrical and physical optics simulation results for the Simons Observatory Large Aperture Telescope. This work was developed as part of the general design process for the telescope; allowing us to evaluate the impact of various design choices on performance metrics and potential systematic effects. The primary goal of the simulations was to evaluate the final design of the reflectors and the cold optics which are now being built. We describe non-sequential ray tracing used to inform the design of the cold optics, including absorbers internal to each optics tube. We discuss ray tracing simulations of the telescope structure that allow us to determine geometries that minimize detector loading and mitigate spurious near-field effects that have not been resolved by the internal baffling. We also describe physical optics simulations, performed over a range of frequencies and field locations, that produce estimates of monochromatic far field beam patterns which in turn are used to gauge general optical performance. Finally, we describe simulations that shed light on beam sidelobes from panel gap diffraction.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Recent Hydrodynamic Modeling Enhancements in OpenFAST: Preprint

To improve the hydrodynamic modeling capabilities of the offshore wind design and modeling tool OpenFAST, a restructuring of the HydroDyn hydrodynamics module was undertaken with several new features implemented. The generation of the wave field is now separated from HydroDyn into a new module called SeaState. Unlike previous versions of HydroDyn, which precomputed the wave kinematics at the undisplaced positions of the hydrodynamic nodes, the new SeaState module computes the complete time history of the wave field at the vertices of a user-defined wave grid. During the simulation, the wave kinematics at any point within the grid can be efficiently interpolated, allowing the strip-theory wave loads to be evaluated based on the wave kinematics at the displaced structure position. A phase correction was also implemented for the potential-flow wave-exciting loads to account for large structure displacements. Several wave-stretching methods were implemented for the strip-theory solution along with a wave-load redistribution method that ensures smooth variation of the nodal loads as the nodes of a discrete hydrodynamic mesh enter and exit the water. The load smoothing is included to avoid the excitation of unphysical high-frequency structural vibration during hydroelastic simulations. The MacCamy-Fuchs diffraction correction for the strip-theory solution and the capability to insert a constrained NewWave into extreme stochastic sea states with directional spreading were also added. The present article documents the formulations of the new improvements to HydroDyn with example applications and numerical results.

constrained wave↗

Direct numerical simulation of mechanical response in synthetic additively manufactured microstructures

Additive manufacturing (AM) processes for metals can yield as-built microstructures that vary significantly from their cast or wrought counterparts. These microstructural variations can in turn, have profound effects on the properties of a component. Here, a modeling methodology is presented to investigate microstructurally-influenced mechanical response in additively manufactured structures via direct numeral simulation. Three-dimensional, synthetic voxelized microstructures are generated by kinetic Monte Carlo (kMC) additive manufacturing process simulations performed at four scan speeds to create a thin-wall cylindrical geometry notionally constructed using a concentric-pathed directed energy deposition AM process. The kMC simulations utilize a steady-state molten pool geometry that is held constant throughout the study. Resultant microstructures are mapped onto a highly-refined conformal finite-element mesh of a part geometry. A grain-scale anisotropic crystal elasticity model is then used to represent the constitutive response of each grain. Here, the response of the structure subjected to relatively simple load conditions is studied in order to provide understanding of both the influence of AM processing on microstructure as well as the microstructure's influence on the macroscale mechanical response.

42 ENGINEERING↗