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At least 1,297 records · Page 72

Evolution of Thyroglobulin Loop Kinetics in EpCAM

Epithelial cell-activating molecule (EpCAM) is an important cancer biomarker and therapeutic target given its elevated expression in epithelial cancers. EpCAM is a type I transmembrane protein that forms cis-dimers along the thyroglobulin type-1A-like domain (TYD) in the extracellular region. The thyroglobulin loop (TY loop) within the TYD is structurally dynamic in the monomer state of human EpCAM, binding reversibly to a TYD site. However, it is not known if this flexibility is prevalent across different species. Here, we conduct over 17 μs of all-atom molecular dynamics simulations to study EpCAM TY loop kinetics of five different species, including human, mouse, chicken, frog, and fish. We find that the TY loop remains dynamic across evolution. In addition to the TYD binding site, we discover a second binding site for the TY loop in the C-terminal domain (CTD). Calculations of the dissociation rate constants from the simulation trajectories suggest a differential binding pattern of fish EpCAM and other organisms. Whereas fish TY loop has comparable binding for both TYD and CTD sites, the TY loops of other species preferably bind the TYD site. A hybrid construct of fish EpCAM with human TY loop restores the TYD binding preference, suggesting robust effects of the TY loop sequence on its dynamic behavior. Our findings provide insights into the structural dynamics of EpCAM and its implication in physiological functions.

59 BASIC BIOLOGICAL SCIENCES↗

Analog Quantum Simulation of the Dynamics of Open Quantum Systems with Quantum Dots and Microelectronic Circuits

We introduce a general setup for the analog quantum simulation of the dynamics of open quantum systems based on semiconductor quantum dots electrically connected to a chain of quantum RLC electronic circuits. The dots are chosen to be in the regime of spin-charge hybridization to enhance their sensitivity to the RLC circuits while mitigating the detrimental effects of unwanted noise. In this context, we establish an experimentally realizable map between the hybrid system and a qubit coupled to thermal harmonic environments of arbitrary complexity that enables the analog quantum simulation of open quantum systems. We assess the utility of the simulator by numerically exact emulations that indicate that the experimental setup can faithfully mimic the intended target even in the presence of its natural inherent noise. We further provide a detailed analysis of the physical requirements on the quantum dots and the RLC circuits needed to experimentally realize this proposal that indicates that the simulator can be created with existing technology. The approach can exactly capture the effects of highly structured non-Markovian quantum environments typical of photosynthesis and chemical dynamics, and offer clear potential advantages over conventional and even quantum computation. The proposal opens a general path for effective quantum dynamics simulations based on semiconductor quantum dots.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Hydrodynamic Modelling for Tidal Energy Kites: Cooperative Research and Development Final Report, CRADA Number CRD-24-30123

The primary goal of the work is to improve accuracy of hydrodynamic loads acting on the lifting surface of the kite turbine due to complex air-water-lifting body interaction in a low-order numerical model using high-fidelity numerical input. The result of this study will help the Participant better design control algorithms for the kite turbine so that the turbine can harvest more energy while maintaining stability of the platform as well as its reliability. The use of hydrodynamic coefficients/load components from computational fluid dynamic simulation will inform better inputs for a medium-fidelity dynamic model (specifically an OrcaFlex model) which is intended for use in rapid design iterations in the design process.

16 TIDAL AND WAVE POWER↗

High-Fidelity Simulations of a Quadrotor Vehicle for Urban Air Mobility

High-fidelity computational fluid dynamics simulations have been carried out to analyze NASA’s quadrotor air taxi concept for urban air mobility. High-order accurate schemes, dual-time stepping, and the delayed detached-eddy simulation model have been employed. The flow solver has been loosely coupled with the rotorcraft comprehensive analysis code. The vehicle simulated is a six-passenger quadrotor for air taxi operations. The quadrotor has been simulated in hover and cruise, with flight conditions representative of an air taxi mission. Initially, the quadcopter vehicle is analyzed using low-fidelity tools. Then, a complete analysis using high-fidelity simulations of the quadcopter is performed in conjunction with collective pitch control. Airloads, wake geometry, and performance are studied and compared. A comparison between isolated rotors and complete vehicle simulations is presented. NASA’s quadrotor is one of NASA’s concept vehicles designed in support of aircraft development for vertical take-off and landing air taxi operations.

ARMD↗

Signatures of electronic and nuclear coherences in ultrafast molecular x-ray and electron diffraction

Femtosecond x-ray and electron diffraction hold promise to image the evolving structures of single molecules. We present a unified quantum-electrodynamical formulation of diffraction signals, based on the exact many-body nuclear + electronic wavefunction that can be extracted from quantum chemistry simulations. This gives a framework for analyzing various approximate molecular dynamics simulations. We show that the complete description of ultrafast diffraction signals contains interesting contributions involving mixed elastic and inelastic scattered photons that are usually masked by other larger contributions and are neglected. These terms include overlaps of nuclear wavepackets between different electronic states that provide an electronic decoherence mechanism and are important for the time-resolved imaging of conical intersections.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Quantum and classical spin dynamics across temperature scales in the S = 1 / 2 Heisenberg antiferromagnet

Using the framework of semiclassical Landau-Lifshitz dynamics (LLD), we conduct a systematic investigation of the temperature-dependent spin dynamics in the S = 1 / 2 Heisenberg square-lattice antiferromagnet (SAFM). By performing inelastic neutron scattering measurements on Zn 2 VO ( PO 4 ) 2 (ZVPO) and corresponding finite-temperature spin dynamics simulations based on LLD, we present a comprehensive analysis that bridges quantum and classical spin dynamics over a broad temperature range. First, remarkable agreement between experimental data and LLD simulations is found in the paramagnetic phase of ZVPO, demonstrating the capability of LLD in accurately determining the spin Hamiltonian of S = 1 / 2 systems and capturing the quantum-to-classical crossover of their spin dynamics. Second, by analyzing the discrepancies between the experimental data and the LLD simulations at lower temperatures, we determine the experimental temperature dependence of the quantum effects in the excitation spectrum of the S = 1 / 2 SAFM: the quantum renormalization factor for the magnon energies and the quantum continuum above the one-magnon bands. Notably, the emergence of each quantum effect is found to correlate with the formation of three-dimensional long-range order. This work demonstrates the utility of LLD in gaining experimental insights into the temperature-induced modifications of quantum spin dynamics and their convergence towards classical expectations at higher temperatures. This motivates further applications to more challenging quantum antiferromagnets dominated by stronger quantum fluctuations. Published by the American Physical Society 2024

36 MATERIALS SCIENCE↗

Terrain-Influenced Winds and Fire-Fire Interactions in Wildland Fire Simulations [Dissertation]

Ensemble-based approaches to prescribed fire planning cannot be supported by computational fluid dynamics based models like FIRETEC and the Wildland-Urban Interface Fire Dynamics Simulator (WFDS) because they are too computationally expensive and cannot leverage large eddy simulation approaches like CAWFE and WRF-SFIRE because they have too coarse of resolution. QUIC-Fire was developed to fill this gap but it cannot currently address complex terrain, that is typical for instance in the Western United States. This dissertation describes a variety of improvements made to QUIC-Fire and its various incorporated algorithms in an effort to make it a viable tool in simulating wildland and prescribed fires on terrain. The modifications made to QUIC-Fire are described in three chapters. The first chapter describes the extension of the diagnostic wind model QUIC-URB, the wind engine of QUIC-Fire, to a terrain-following coordinate system. The terraininfluenced winds it generates are analyzed and compared. In particular, this chapter presents the mathematical derivation of the wind solver leading to a linear system of equations that are solved through the successive over-relaxation method. The model is validated against a standard test used in previous works (the Askervein Hill) and against a new dataset from measurements in the Socorro Mountains, New Mexico. The terrain-following implementation captures the correct phenomenology for the isolated Askervein Hill, with a wind speed up at the top of the hill. The model agrees well with measurements on the upwind side of the peak, but overestimates speed-up on the downwind side of the hill. This is due to the inability of the model to generate flow separation and wake-eddy dynamics. On a common laptop, the divergence-free wind field is obtained in 6 s, making the solver appealing for coupled fire-atmosphere simulations. The Socorro Mountain is highly complex, with many cliff faces, peaks, and valleys. Although the model captures the magnitude and direction of inlet and outlet areas of the domain, it performs rather poorly in the valley region and in the regions near the steep cliffs. Hence, the model shows good agreement with data in areas of open sloped terrain but lacks in areas where flow separation and thermally driven effects may be present (neither effect is addressed in this work). In the second chapter the implementation of the terrain-following version of QUIC-URB into QUIC-Fire, and the necessary changes needed to include terrain are described. No changes to the underlying fire spread algorithm are made other than what is required to correctly account for the inclusion of terrain. Previously published FIRETEC results that use five different topographies that share the same centerline profile are compared to simulation results from the modified QUIC-Fire that use the same topographies and fuels. QUIC-Fire results show overall similar behaviors in terms of how the topographies affect fire shapes and trends in spread rates. Due to the terrain-following version of QUIC-URB being unable to generate flow separations at the crest of hills, fire spread rates in these regions across all topographies are over-predicted when compared to FIRETEC. Lateral fire growth shows similar trends with FIRETEC between topographies but does not capture the increase in spread due to a diagonal interface between grassland and forested fuel region of the domain. These results suggest that there are three algorithms within QUIC-Fire that could use improvement: how flame tilt angle is accounted for, the incorporation of non-local drag effects, and the inclusion of the wake-eddy parameterizations that are used in QUIC-URB. Lastly, the third chapter describes a modification to the initial guess used for the calculation of the QUIC-URB mass-conserved wind solution during fire simulations. The modification is aimed at improving fire-fire interactions in QUIC-Fire simulations. The modification consists of using the solution from the previous timestep as the starting point for the calculation of the solution for the next timestep. Fire-fire interactions is greatly improved by the change but a new source of error is introduced. Due to how plumes are modelled in QUIC-Fire the new solution contains errors where gaps in the plume structure are present. However, these errors are mostly limited to the upper atmosphere, where they do not affect fire behavior at the surface, and their magnitude isn’t significant enough to discount the amount of new fire phenomenology now captured in QUIC-Fire with the change.

58 GEOSCIENCES↗

Recombination of Autodissociated Water Ions in a Nanoscale Pure Water Droplet

The recombination of water ions has diverse scientific and practical implications, ranging from acid-base chemistry and biological systems to planetary environments and applications in fuel cell and carbon conversion technologies. While spatial confinement affects the physicochemical properties of water dynamics, its impact on the recombination process has rarely been studied. In this work, we investigate the dynamics of water, the water ion distribution, and the ion recombination process in water droplets as a function of droplet size through molecular dynamics simulations and adaptive quantum mechanical/molecular mechanical calculations. We compare the dynamics of recombination in water droplet sizes ranging from 100 to 18 000 waters, both in their interiors and on their surfaces. We found that the self-diffusion of water dramatically decreases in droplets with a diameter below 2.2 nm. Using a classical RexPoN force-field, we found that the ions in 1000 H2O's spend almost 50% of the time on the surface and 0.5 nm beneath it with a slight preference for OH- ion to reside longer on the surface. We estimate that, on average, recombination in these drops occurs at 400 ps in 1000 H2O's and 1 ns in 3000 H2O's. We also found that recombination is not limited by the local structure of the surface or the size of the droplet but can be influenced by the geometry of the water wire connecting the ions as they approach each other, which can often prevent recombination. Our results provide insights to the reaction microenvironments presented by nanoscopic water droplets.

Kwon, Soonho↗

Surface Hydroxyls of Imogolite Nanotubes Drive Distinct Structures and Mobility Differentiation of Nanoconfined Water

Abstract Nanoconfined fluids, particularly water, govern subsurface geochemistry, yet the molecular-level mechanisms by which mineral surfaces dictate confined water structure and mobility remain poorly resolved. Here, we combine solution- and solid-state proton (1H) NMR spectroscopy, NMR relaxometry, modulated-gradient spin–echo (MGSE) NMR diffusometry, infrared spectroscopy, and molecular dynamics simulations to demonstrate that surface hydroxyls drive the structural and dynamic differentiation of water in imogolite nanotubes. In saturated suspensions, we observe the coexistence of distinct water 1H environments, each exhibiting significantly reduced mobility, which we attribute to strong interactions with the imogolite surfaces. As more mobile water is removed, long-range water diffusivity in the fibrous solid samples slows to 1.6 × 10–10 m2·s–1 while local fluctuations increase to 3.4 × 10–8 m2·s–1, indicating a significant increase in molecular restriction through surface interactions. Together, our experiments reveal three coexisting populations with varied structures and mobilities, all distinct from liquid bulk water. We resolve a persistent solid-like interfacial layer strongly bound to surface hydroxyls, characterized by an unusually short T2 (<1 ms), and a very close effective 1H–1H distance of ∼1.55 Å between water and the inner-surface silanol group. An inner-core population occupying the inner cavity exhibits an intermediate dynamic regime with restricted axial diffusion, while outer-surface water associated with aluminum hydroxyls retains relatively higher mobility. These results experimentally substantiate a hierarchy of water populations in imogolite and show how surface chemistry dictates the structures and dynamics of confined water.

Fleming, Xander B. [Earth and Environmental Scienc↗

A two-dimensional type I superionic conductor

Superionic conductors (SICs) possess liquid-like ionic diffusivity in the solid state, finding wide applicability from electrolytes in energy storage to materials for thermoelectric energy conversion. Type I SICs (e.g., AgI, Ag 2 Se, etc.) are defined by a first-order transition to the superionic state and have so far been found exclusively in three-dimensional crystal structures. Here, we reveal a two-dimensional type I SIC, α-KAg 3 Se 2 by scattering techniques and complementary simulations. Quasi-elastic neutron scattering and ab initio molecular dynamics simulations confirm that the superionic Ag + ions are confined to sub-nanometre sheets, with the simulated local structure validated by experimental X-ray powder pair-distribution-function analysis. Finally, we demonstrate that the phase transition temperature can be controlled by chemical substitution of the alkali metal ions that comprise the immobile charge-balancing layers. Our work thus extends the known classes of SICs and will facilitate the design of new materials with tailored ionic conductivities and phase transitions.

36 MATERIALS SCIENCE↗

Effects of pore connectivity and tortuosity on the dynamics of fluids confined in sub-nanometer pores

Dynamical behavior of fluids under nano-pore confinement is studied extensively as it has important implications for several industrial as well as geological processes. Pore network in many porous materials exhibits a varied degree of inter connections. The extent of this pore connectivity may affect the structural and dynamical behavior of the confined fluid. However, studies of fluid confinement addressing these effects systematically are lacking. In this paper we report molecular dynamics simulation studies addressing the effects of pore connectivity on the dynamics of two representative fluids – CO 2 and ethane in silicalite by systematically varying the degree of pore connectivity through selectively blocking some pore space with immobile methane molecules. By selectively turning off the pore spaces in the shape of straight, or tortuous zigzag channels, we also probe the effects of pore tortuosity. In general, pore connectivity is found to facilitate both the translational as well as rotational dynamics of both fluids, while the intermolecular modes of vibration in both fluids remain largely unaffected. The effects of providing connections between a set of straight or zigzag channel-like pores are however more nuanced. Pore tortuosity facilitates the rotational motion, but suppresses the translational motion of CO 2 , while its effects on the rotational and translational motion of ethane are less pronounced. The intermolecular vibrational modes of both fluids shift to higher energies with an increase in the number of tortuous pores. The results reported here provide a detailed molecular level understanding of the effects of pore connectivity on the dynamics of fluids and thus have implications for applications like fluid separation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Stratification of polymer mixtures in drying droplets: Hydrodynamics and diffusion

In this work, we study the evaporation-induced stratification of a mixture of short and long polymer chains in a drying droplet using molecular simulations. We systematically investigate the effects of hydrodynamic interactions (HI) on this process by comparing hybrid simulations accounting for HI between polymers through the multiparticle collision dynamics technique with free-draining Langevin dynamics simulations neglecting the same. We find that the dried supraparticle morphologies are homogeneous when HI are included but are stratified in core–shell structures (with the short polymers forming the shell) when HI are neglected. The simulation methodology unambiguously attributes this difference to the treatment of the solvent in the two models. We rationalize the presence (or absence) of stratification by measuring phenomenological multicomponent diffusion coefficients for the polymer mixtures. The diffusion coefficients show the importance of not only solvent backflow but also HI between polymers in controlling the dried supraparticle morphology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Platinum nanoparticle compression: Combining in situ TEM and atomistic modeling

The mechanical behavior of nanoparticles governs their performance and stability in many applications. However, the small sizes of technologically relevant nanoparticles, with diameters in the range of 10 nm or less, significantly complicate experimental examination. These small nanoparticles are difficult to manipulate onto commercial test platforms and deform at loads that are below the typical noise floor of the testing instruments. Here, we synthesized small platinum nanoparticles directly onto a mechanical tester and used a modified nanomanipulator to enhance load resolution to the nanonewton scale. We demonstrated the in situ compression of an 11.5-nm platinum nanoparticle with simultaneous high-resolution measurements of load and particle morphology. Molecular dynamics simulations were performed on similarly sized particles to achieve complementary measurements of load and morphology, along with atomic resolution of dislocations. The experimental and simulation results revealed comparable values for the critical resolved shear stress for failure, 1.28 and 1.15 GPa, respectively. Altogether, this investigation demonstrated the promise of, and some initial results from, the combination of atomistic simulations and in situ experiments with an unprecedented combination of high spatial resolution and high load resolution to understand the behavior of metal nanoparticles under compression.

42 ENGINEERING↗

Mediation of Colloidal Encounter Dynamics by Surface Roughness

Rigorous understanding on the self-assembly of colloidal nanocrystals is crucial to develop tailored nanostructured materials for energy storage, sensing, and optical fields. Despite extensive studies on the self-assembly, a mechanistic understanding of self-assembly under an external field still remains an ongoing challenge. Here, in this work, we used optical tweezers that impose an external attractive force field, resulting in the self-assembly of alpha-phase sodium yttrium fluoride nanocrystals. The dynamic force that is strongly dependent on the surface roughness of the nanocrystals is shown to be a decisive factor for a direct contact between the nanocrystals, manifested by the roughness-dependent hydrodynamic resistivity and Langevin dynamic simulations. Our study provides direct evidence that the role of dynamics is equally important in understanding the self-assembly, which has been rarely observed in the self-assembly in contrast with many studies on the equilibrium forces. These results may have further impact in other fields, such as having explanatory power for the probability of nonclassical crystal growth or the structure of viral spike proteins that affect the probability of viruses binding with cells.

Felsted, Robert G. [Univ. of Washington, Seattle, ↗

Skyrmion formation in Ni-based Janus dihalide monolayers: Interplay between magnetic frustration and Dzyaloshinskii-Moriya interaction

Here we present a comprehensive theory of the magnetic phases in monolayer nickel-based Janus dihalides (NiIBr, NiICl, NiBrCl) through a combination of first-principles calculations and atomistic simulations. Phonon band structure calculations and finite-temperature molecular dynamics simulations show that Ni-dihalide Janus monolayers are stable. The parameters of the interacting spin Hamiltonian extracted from ab initio calculations show that nickel-dihalide Janus monolayers exhibit varying degrees of magnetic frustration together with a large Dzyaloshinskii-Moriya interaction due to their inherent inversion symmetry breaking. The atomistic simulations reveal a delicate interplay between these two competing magnetic interactions in giving rise to skyrmion formation.

36 MATERIALS SCIENCE↗

Dynamic Structure Discovery Applied to the Ion Transport in the Ubiquitous Lithium-ion Battery Electrolyte LP30

The electrolytes of the today omnipresent lithium-ion batteries (LIBs) have for more than 25 years been based upon 1 M LiPF 6 in a 50:50 EC:DMC mixture—commonly known as LP30. The success of the basic design of the LP30 electrolyte, with many variations and additions made over the years, is unchallenged. Yet, some molecular level fundamentals of LP30 are surprisingly elusive: the structure of the first solvation shell of the Li + cation is still a topic of current debate; the details of the dynamics are not fully understood; the interpretation of structural and dynamic properties is highly dependent on the analysis methods used; the contributions by different species to the ion transport and the energetics involved are not established. We here apply dynamic structure discovery analysis as implemented in CHAMPION to molecular dynamics simulation trajectories to bring new light on the structure and dynamics within LP30 and especially the (Li + ) ion transport to rationalize further development of LIB electrolytes.

25 ENERGY STORAGE↗

A compilation of spacecraft loads data from four Titan Centaur Launch Vehicle flights. Volume 1: Acoustics data

The payloads carried by the first four Titan Centaur launch vehicle flights were, a Viking spacecraft dynamic simulator, the Helios A spacecraft, and the two Viking spacecraft. Dynamic loads data were accumulated from these four flights for application to the Viking spacecraft. The accoustics data include time histories and spectral analysis plots of accoustic pressure measurements made in the Centaur and payload compartment during launch flight. Summary plots are presented to show composite spectra for liftoff and Mach 1/Max Q periods of flight.

Kachadourian, G.↗

Voice interactive electronic warning systems (VIEWS) - An applied approach to voice technology in the helicopter cockpit

The cockpit has been one of the most rapidly changing areas of new aircraft design over the past thirty years. In connection with these developments, a pilot can now be considered a decision maker/system manager as well as a vehicle controller. There is, however, a trend towards an information overload in the cockpit, and information processing problems begin to occur for the rotorcraft pilot. One approach to overcome the arising difficulties is based on the utilization of voice technology to improve the information transfer rate in the cockpit with respect to both input and output. Attention is given to the background of speech technology, the application of speech technology within the cockpit, voice interactive electronic warning system (VIEWS) simulation, and methodology. Information subsystems are considered along with a dynamic simulation study, and data collection.

Voorhees, J. W.↗