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DOE OSTI2020

Phonon-mediated lipid raft formation in biological membranes

Short-wavelength collective molecular motions, also known as phonons, have recently attracted much interest in revealing dynamic properties of biological membranes through the use of neutron and x-ray scattering, infrared and Raman spectroscopies, and molecular dynamics simulations. Experimentally detecting unique vibrational patterns such as, shear phonon excitations, viscoelastic crossovers, transverse acoustic phonon gaps, and continuous and truncated optical phonon modes in cellular membranes, to name a few, has proven non-trivial. Here, we review recent advances in liquid thermodynamics that have resulted in the development of the phonon theory of 1 liquids. The theory has important predictions regarding the shear vibrational spectra of fluids, namely the emergence of viscoelastic crossovers and transverse acoustic phonon gaps. Furthermore, we show that these vibrational patterns are common in soft (non-crystalline) materials, including, but not limited to liquids, colloids, liquid crystals (mesogens), block copolymers, and biological membranes. The existence of viscoelastic crossovers and acoustic phonon gaps define the self-diffusion properties of cellular membranes and provide a molecular picture of the transient nature of lipid rafts.1 Importantly, the timescales (picoseconds) for the formation and dissolution of transient lipid rafts match the lifetime of the formation and breakdown of interfacial water hydrogen bonds. Apart from acoustic propagating phonon modes, biological membranes can also support more energetic non-propagating optical phonon excitations, also known as standing waves or breathing modes. Importantly, optical phonons can be truncated due to the existence of finite size nanodomains made up of strongly correlated lipid-cholesterol molecular pairs. These strongly coupled molecular pairs can serve as nucleation centers for the formation of stable rafts at larger length scales, due to correlations of spontaneous fluctuations (Onsager’s regression hypothesis). Finally and importantly, molecular level viscoelastic crossovers, acoustic phonon gaps, and continuous and truncated optical phonon modes may offer insights as to how lipid-lipid and lipid-protein interactions enable biological function.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Understanding Viscoelasticity of an Entangled Silicone Copolymer via Coarse-Grained Molecular Dynamics Simulations

Entangled dynamics is important for understanding rheological properties of long-chain polymers. For entangled homopolymers, the classic tube-reptation model and its refinements have been successfully applied to quantify properties like diffusion coefficient and zero-rate viscosity. However, the application of such models to copolymers has been limited despite scientific and industrial importance. Here, we study the entangled melt dynamics of poly(dimethyl-co-diphenyl)siloxane random copolymer for a range of mean-composition-ratio ϕ of the diphenyl component via long-term molecular dynamics simulation with a recently developed coarse-grained model. We found that the segmental relaxation is heterogeneous at the monomeric level because of compositional fluctuations. However, at the chain-entanglement level and higher length scales, the viscoelastic response is homogeneous with compositional dependence only through the overall diphenyl fraction ϕ. The relaxation modulus of the entangled copolymer melt conforms to the Likhtman–McLeish model, and the viscosity predicted using our current coarse-grained parameters is in good quantitative agreement with experimental data.

Copolymers↗

DOE OSTI2022

Microstructural pattern formation during liquid metal dealloying: Phase-field simulations and theoretical analyses

In recent years, liquid metal dealloying has emerged as a promising material processing method to generate micro- and nanoscale bicontinuous or porous structures. Most previous studies focused on the experimental characterization of the dealloying process and on the properties of the dealloyed materials, leaving the theoretical study incomplete to fully understand the fundamental mechanisms of the liquid metal dealloying process. In this paper, we use theoretical models and phase-field simulations to clarify the kinetics and pattern formation during liquid metal dealloying. Our investigation starts from a theoretical analysis of the 1D dissolution of a binary precursor alloy, which reveals that the 1D dissolution process involves two regimes. In the first regime, due to the low solubility of one of the elements in the melt, it accumulates at the solid-liquid interface, which reduces the dissolution kinetics. In the second regime, the interface kinetics reaches a stationary regime where both elements of the precursor alloy dissolve into the melt. Previous works revealed that in the early dealloying stage, the dealloying front is destabilized by an interfacial spinodal decomposition, which triggers the formation of interconnected ligaments. Here we extend this line of work by proposing a linear stability analysis able to predict the initial length scale of the ligaments formed in the initial stage of the dealloying. Combining this analysis with the 1D dissolution model proposed here enables us to better understand the initial conditions (composition of the precursor alloy and the melt) leading to a planar dissolution without interface destabilization. Finally, we report a strong influence of solid-state diffusion on dealloying. Although the solid-state diffusivity is four to five orders of magnitude smaller than in the liquid phase, it is found to affect both dissolution kinetics and ligament morphologies.

36 MATERIALS SCIENCE↗

DOE OSTI2025

MMMnet: A Neural Network Surrogate for Real-Time Transport Prediction Based on the Updated Multi-Mode Model

The Multi-Mode Model (MMM) is a physics-based anomalous transport model integrated into TRANSP for predicting electron and ion thermal transport, electron and impurity particle transport, and toroidal and poloidal momentum transport. While MMM provides valuable predictive capabilities, its computational cost, although manageable for standard simulations, is too high for real-time control applications. MMMnet, a neural network-based surrogate model, is developed to address this challenge by significantly reducing computation time while maintaining high accuracy. Trained on TRANSP simulations of DIII-D discharges, MMMnet incorporates an updated version of MMM (9.0.10) with enhanced physics, including isotopic effects, plasma shaping via effective magnetic shear, unified correlation lengths for ion-scale modes, and a new physics-based model for the electromagnetic electron temperature gradient mode. A key advancement is MMMnet’s ability to predict all six transport coefficients, providing a comprehensive representation of plasma transport dynamics. MMMnet achieves a two-order-of-magnitude speed improvement while maintaining strong correlation with MMM diffusivities, making it well-suited for real-time tokamak control and scenario optimization.

DIII-D↗

NASA NTRS1978

On the propagation of cosmic rays in the Galaxy

Cosmic ray propagation in the Galaxy is examined within the framework of the leaky-box model, whereby phenomenological aspects of diffusion and propagation are related to the physical properties of the interstellar medium. The model is parameterized by data on composition, spectra, spectral change as a function of energy, and cosmic ray particle lifetime. It is assumed that electrons and nucleons have a common source within the Galaxy (probably associated with supernova remnants). Lifetime data and leakage length are compared with radio synchrotron and gamma-ray data to establish a place of origin for cosmic rays observed at earth, i.e., at a radius of 0.5-1.0 kpc from earth. It is noted that if the escape length becomes energy independent, all nuclear spectra will flatten, while the electron spectrum remains unchanged.

Ormes, J.↗

NASA NTRS2003

Effect of Crucible Diameter Reduction on the Convection, Macrosegregation, and Dendritic Morphology during Directional Solidification of Pb-2.2 Wt Pct Sb Alloy

The Pb-2.2 wt pct Sb alloy has been directionally solidified in 1-, 2-, 3-, and 7-mm-diameter crucibles with planar and dendritic liquid-solid interface orphology. For plane front solidification, the experimentally observed macrosegregation along the solidified length follows the relationship proposed by Favier. Application of a 0.4 T transverse magnetic field has no effect on the extent of convection. Reducing the ampoule diameter appears to decrease the extent of convection. However, extensive convection is still present even in the 1-mm-diameter crucible. An extrapolation of the observed behavior indicated that nearly diffusive transport conditions require ampoules that are about 40 microns in diameter. Reduction of the crucible diameter does not appear to have any significant effect on the primary dendrite spacing. However, it results in considerable distortion of the dendrite morphology and ordering. This is especially true for the 1-mm diameter samples.

Chen, Jun↗

DOE OSTI2015

Molecular dynamics force-field refinement against quasi-elastic neutron scattering data

Quasi-elastic neutron scattering (QENS) is one of the experimental techniques of choice for probing the dynamics at length and time scales that are also in the realm of full-atom molecular dynamics (MD) simulations. This overlap enables extension of current fitting methods that use time-independent equilibrium measurements to new methods fitting against dynamics data. We present an algorithm that fits simulation-derived incoherent dynamical structure factors against QENS data probing the diffusive dynamics of the system. We showcase the difficulties inherent to this type of fitting problem, namely, the disparity between simulation and experiment environment, as well as limitations in the simulation due to incomplete sampling of phase space. We discuss a methodology to overcome these difficulties and apply it to a set of full-atom MD simulations for the purpose of refining the force-field parameter governing the activation energy of methyl rotation in the octa-methyl polyhedral oligomeric silsesquioxane molecule. Our optimal simulated activation energy agrees with the experimentally derived value up to a 5% difference, well within experimental error. We believe the method will find applicability to other types of diffusive motions and other representation of the systems such as coarse-grain models where empirical fitting is essential. In addition, the refinement method can be extended to the coherent dynamic structure factor with no additional effort.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Isopycnal Eddy Diffusivities and Critical Layers in the Kuroshio Extension from an Eddying Ocean Model

High spatial resolution isopycnal diffusivities are estimated in the Kuroshio Extension (KE) region (28°–40°N, 120°–190°E) from a global 1/10° Parallel Ocean Program (POP) simulation. The numerical float tracks are binned using a clustering approach. The number of tracks in each bin is thus roughly the same leading to diffusivity estimates that converge better than those in bins defined by a regular geographic grid. Cross-stream diffusivities are elevated in the southern recirculation gyre region, near topographic obstacles and downstream in the KE jet, where the flow has weakened. Along-stream diffusivities, which are much larger than cross-stream diffusivities, correlate well with the magnitudes of eddy velocity. The KE jet suppresses cross-stream mixing only in some longitude ranges. This study estimates the critical layer depth both from linear local baroclinic instability analysis and from eddy phase speeds in the POP model using the Radon transform. The latter is a better predictor of large mixing length in the cross-stream direction. Critical layer theory is most applicable in the intense jet regions away from topography.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Investigation of Scale-Dependent Groundwater/Surface-water Exchange in Rivers by Gradient Self-Potential Logging: Numerical Modeling and Field Experiments

Exchanges of groundwater and surface-water are fundamental to a wide range of water-supply and water-quality management issues but challenging to map beyond the reach scale. Waterborne gradient self-potential (SP) measurements are directly sensitive to water flow through riverbed sediments and can be used to infer exchange locations, direction (gain versus loss), scale, and relative changes, but to date applications to river corridor hydrology are limited. Numerical modeling and field experiments were therefore performed herein, each emphasizing waterborne gradient SP logging for identifying and locating focused vertical groundwater discharge (surface-water gain) and recharge (surface-water loss) in a river. Two and three-dimensional numerical models were constructed to simulate the polarities, appearances, and peak amplitudes of streaming-potential and electric-field anomalies on a riverbed and in the surface-water that were attributable to steady-state vertical fluxes of groundwater through high-permeability conduits in the riverbed. Effects of varied hydraulic length-scale of exchange and surface-water depth were tested through numerical modeling. Modeling results aided in data acquisition and interpretation for three repeated field experiments performed along a 1.5–2.0 km reach of the Quashnet River in Cape Cod, Massachusetts, where focused, meter-scale groundwater discharges occur at discrete locations within otherwise ubiquitous and more diffuse groundwater upwelling conditions. Strong gradient SP anomalies were repeatedly measured in the Quashnet River at previously confirmed locations of focused groundwater discharge, showing the efficacy of waterborne gradient SP logging in identifying and characterizing groundwater/surface water exchange dynamics at multiple river network scales.

Engineering↗

DOE OSTI2022

Numerical and Experimental Investigations on the Ignition Behavior of OME

On the path towards climate-neutral future mobility, the usage of synthetic fuels derived from renewable power sources, so-called e-fuels, will be necessary. Oxygenated e-fuels, which contain oxygen in their chemical structure, not only have the potential to realize a climate-neutral powertrain, but also to burn more cleanly in terms of soot formation. Polyoxymethylene dimethyl ethers (PODE or OMEs) are a frequently discussed representative of such combustibles. However, to operate compression ignition engines with these fuels achieving maximum efficiency and minimum emissions, the physical-chemical behavior of OMEs needs to be understood and quantified. Especially the detailed characterization of physical and chemical properties of the spray is of utmost importance for the optimization of the injection and the mixture formation process. The presented work aimed to develop a comprehensive CFD model to specify the differences between OMEs and dodecane, which served as a reference diesel-like fuel, with regards to spray atomization, mixing and auto-ignition for single- and multi-injection patterns. The simulation results were validated against experimental data from a high-temperature and high-pressure combustion vessel. The sprays’ liquid and vapor phase penetration were measured with Mie-scattering and schlieren-imaging as well as diffuse back illumination and Rayleigh-scattering for both fuels. To characterize the ignition process and the flame propagation, measurements of the OH* chemiluminescence of the flame were carried out. Significant differences in the ignition behavior between OMEs and dodecane could be identified in both experiments and CFD simulations. Liquid penetration as well as flame lift-off length are shown to be consistently longer for OMEs. Zones of high reaction activity differ substantially for the two fuels: Along the spray center axis for OMEs and at the shear boundary layers of fuel and ambient air for dodecane. Additionally, the transient behavior of high temperature reactions for OME is predicted to be much faster.

33 ADVANCED PROPULSION SYSTEMS↗

NASA NTRS1987

Analysis of non-premixed turbulent reacting flows

Studies of chemical reactions occurring in turbulent flows are important in the understanding of combustion and other applications. Current numerical methods are limited in their applications due to the numerical resolution required to completely capture all length scales, but, despite the fact that realistic combustion cannot be solved completely, numerical simulations can be used to give insight into the interaction between the processes of turbulence and chemical reaction. The objective was to investigate the effects of turbulent motion on the effects of chemical reaction to gain some insight on the interaction of turbulence, molecular diffusion, and chemical reaction to support modeling efforts. A direct turbulence simulation spectral code was modified to include the effects of chemical reaction and applied to an initial value problem of chemical reaction between non-premixed species. The influence of hydrodynamics on the instantaneous structure of the reaction was investigated. The local scalar dissipation rates and the local reaction rates were examined to determine the influence of vorticity or rate of strain on the reaction and the structure of the scalar field.

Leonard, Andy D.↗

NASA NTRS2002

Transient Mixing Driven by Buoyancy Flows

Mixing driven by buoyancy-induced flows is of particular interest to microgravity processes, as the body force that governs the intensity of flow fields can be directly controlled. We consider a model experimental system to explore the dynamics of mixing which employs two miscible liquids inside a cavity separated initially by a divider. The two liquids are oriented vertically inside a rectangular cavity with constant width and height, and varying depths to span the range of a Hele-Shaw cell to a 3-[) configuration. The two miscible liquids can be sufficiently diluted and died, for example water and deuterium oxide, such that a distinct interface exists across the divider. The transient mixing characteristic of the two fluids is addressed by following the Lagrangian history of the interface for various aspect ratios in the z-plane (depth variation) as well as a range of pulling velocities of the divider. The mixing characteristics of the two fluids are quantified from measurement of the length stretch of the interface and its flow field using respectively image processing techniques and Particle Imaging Velocimetry. Scaling analysis shows that the length stretch depends on four governing parameters, namely the Grashof number (Gr), Schmidt number (Sc), aspect ratio (Ar), and Reynolds number (Re). Variation of the Schmidt number is taken into account through thermophysical property variation. Thus our problem reduces to a codimension three bifurcation in parametric space for Gr, Ar, and Re. Our experimental results show that for Gr on the order of 106 and a nominal cavity aspect ratio Ar = 0.2, the net effect of removal of the divider and the overwhelming buoyancy force causes an overturning motion which stretches and folds the interface to produce ml internal breakwave. The structure of the breakwave is similar to the ubiquitous Rayleigh-Taylor instability morphology. The breakwave is dissipated either through internal or wall collision depending on the impulsive velocity of the divider as prescribed by the Reynolds number. The decay of the collision event occurs through sloshing oscillations over a short time scale. The two fluids then become stably stratified with a diffusive band at the interface indicating local mass transport. The local bifurcation of the internal breakwave is investigated as a function of aspect ratio. Results show that for narrow cavities on the order of 2mm (Ar = 0.04) folding does not occur, the interface only stretches. As the cavity size increases folding occurs through a supercritical bifurcation. Insight into the mechanism of folding is obtained from measurement of the flow field which shows that in the neighborhood of the folding event, there exists hyperbolic points caused by multiple vortex interactions. The global length stretch of the interface as a function of time is nearly Gaussian; calculations of finite-time Liapunov exponents as well as construction of horseshoe maps indicate the likelihood of a chaotic transient.

W.M.B. Duval↗

DOE OSTI2022

Polyethylene in Dead-End Silica Nanopores: Forces and Mobility from Non-Equilibrium Statistical Mechanics and Exchange Spectroscopy Nuclear Magnetic Resonance

Billions of tons of plastic have been produced, and only a small fraction of this has been recycled. Tennakoon et al. [Nature Catalysis 3, 893 (2020)] developed a catalyst that repeatedly cleaves C 10 –C 30 hydrocarbons from the end of a polyethylene chain. The reaction occurs at a Pt nanoparticle at the base of a cylindrical silica mesopore with a diameter of 2 nm and a length of 110 nm. Portions of the polymer situated inside the pore can be differentiated from those outside using 13 C nuclear magnetic resonance (NMR), allowing the dynamics and extent of polymer threading to be monitored using two-dimensional (2D) exchange spectroscopy NMR. Here we construct a Fokker–Planck equation for the polymer dynamics by assuming a reptation diffusivity and a graduated adsorption free energy that depends linearly on the depth of polymer penetration in the pore. The solutions allow us to predict the intensities of the 2D NMR resonances as a function of time. We use the solutions to extract a polymer diffusivity at each temperature and estimate the per-segment desorption free energy, enthalpy, and entropy. Random and systematic errors are examined to test key assumptions in the theory and interpretation of the experiments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Effects of q-profile structure on turbulence spreading: A fluctuation intensity transport analysis

This paper studies effects of q-profile structure on turbulence spreading. It reports results of numerical experiments using global gyrokinetic simulations. We examine propagation of turbulence, triggered by an identical linear instability in a source region, into an adjacent, linearly stable region with variable q-profile. The numerical experiments are designed so as to separate the physics of turbulence spreading from that of linear stability. The strength of turbulence spreading is measured by the penetration depth of turbulence. Dynamics of spreading are elucidated by fluctuation intensity balance analysis, using a model intensity evolution equation which retains nonlinear diffusion and damping, and linear growth. It is found that turbulence spreading is strongly affected by magnetic shear s, but is hardly altered by the safety factor q itself. There is an optimal range of modest magnetic shear which maximizes turbulence spreading. For high to modest shear values, the spreading is enhanced by the increase of the mode correlation length with decreasing magnetic shear. However, the efficiency of spreading drops for sufficiently low magnetic shear even though the mode correlation length is comparable to that for the case of optimal magnetic shear. The reduction of spreading is attributed to the increase in time required for the requisite nonlinear mode-mode interactions. The effect of increased interaction time dominates that of increased mode correlation length. Our findings of the reduction of spreading and the increase in interaction time at weak magnetic shear are consistent with the well-known benefit of weak or reversed magnetic shear for core confinement enhancement. Weak shear is shown to promote locality, as well as stability.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2017

Hydrodynamic tails and a fluctuation bound on the bulk viscosity

Here, we study the small frequency behavior of the bulk viscosity spectral function using stochastic fluid dynamics. We obtain a number of model independent results, including the long-time tail of the bulk stress correlation function and the leading nonanalyticity of the spectral function at small frequency. We also establish a lower bound on the bulk viscosity which is weakly dependent on assumptions regarding the range of applicability of fluid dynamics. The bound on the bulk viscosity $ζ$ scales as $ζ_{min} ~( P - \frac{2}{3}\mathscr{E}) ^2Σ_iD_i^{-2}$, where $D_i$ are the diffusion constants for energy and momentum and $P - \frac{2}{3}\mathscr{E}$, where $P$ is the pressure and $\mathscr{E}$ is the energy density, is a measure of scale breaking. Applied to the cold Fermi gas near unitarity, $|λ/a_s| ≳ 1$, where $λ$ is the thermal de Broglie wavelength and $a_s$ is the s-wave scattering length, this bound implies that the ratio of bulk viscosity to entropy density satisfies $ζ/s ≳ 0.1ℏ/k_B$. Here, $ℏ$ is Planck's constant and $k_B$ is Boltzmann's constant.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2020

Electron-electron interactions in low-dimensional Si:P delta layers

Scientists have long studied the physics of highly disordered conducting systems, seeking to understand the multitude of quantum phenomena that govern how electrons move through material systems. Recently, research into silicon-based quantum computing has made disordered conducting systems, such as Si:P monolayers embedded in isotopically pure Si, technically relevant. Consequently, applying and advancing the theoretical frameworks developed to describe electron behavior in disordered systems is a necessary objective in this field of research. This study investigates key components of dopant-based Si quantum computing devices: embedded regions of highly doped delta layers (δ layers). We examine the transport behavior and the electron-electron interaction (EEI) physics in embedded Si:P δ layers by means of self-consistent magnetotransport measurements. Parameters associated with the electronic transport offer a meaningful quantitative characterization of δ-layer quality and dopant diffusion. In addition, by examining EEI behaviors in a set of samples with embedded Si:P δ layers produced with different PH3 exposure procedures prior to Si encapsulation, we show how details of material synthesis affect the dimensionality of charge carrier interactions in embedded Si:P δ layers. Furthermore, the relationship between δ-layer confinement and EEI screening lengths is established here. This understanding will help validate important models used for device simulation and design and lead to improvements in the control of electrostatic gating of and tunneling transport through Si:P single atom transistors.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2017

Prediction of Thermal Transport Properties of Materials with Microstructural Complexity

This project aims at overcoming the major obstacle standing in the way of progress in dynamic multiscale simulation, which is the lack of a concurrent atomistic-continuum method that allows phonons, heat and defects to pass through the atomistic-continuum interface. The research has led to the development of a concurrent atomistic-continuum (CAC) methodology for multiscale simulations of materials microstructural, mechanical and thermal transport behavior. Its efficacy has been tested and demonstrated through simulations of dislocation dynamics and phonon transport coupled with microstructural evolution in a variety of materials and through providing visual evidences of the nature of phonon transport, such as showing the propagation of heat pulses in single and polycrystalline solids is partially ballistic and partially diffusive. In addition to providing understanding on phonon scattering with phase interface and with grain boundaries, the research has contributed a multiscale simulation tool for understanding of the behavior of complex materials and has demonstrated the capability of the tool in simulating the dynamic, in situ experimental studies of nonequilibrium transient transport processes in material samples that are at length scales typically inaccessible by atomistically resolved methods.

36 MATERIALS SCIENCE↗

NASA NTRS1978

Turbulent convection within rapidly rotating superadiabatic fluids with horizontal temperature gradients

A model is developed for small scale thermally driven turbulent convection in rapidly rotating systems. The Boussinesq equations of adiabatic and inviscid flow are perturbed about a basic state which is superadiabatic and which contains a horizontal temperature gradient balanced by a geostrophic wind. The growth rates and length scales of the most unstable modes are determined. It is found that these modes are either zonally or latitudinally symmetric, depending on the latitude and the horizontal temperature gradient. The transports of heat and momentum by the modes are computed. The linear amplitudes are assumed to be limited by shear instability. The model predicts a latitude dependent eddy diffusivity. The applicability of the model to astrophysical and planetary bodies is briefly discussed.

Flasar, F. M.↗