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At least 577 records · Page 32

Continuous momentum dependence in the dynamical cluster approximation

The dynamical cluster approximation (DCA) is a quantum cluster extension to the single-site dynamical mean-field theory that incorporates spatially nonlocal dynamic correlations systematically and nonperturbatively. The DCA + algorithm addresses the cluster shape dependence of the DCA and improves the convergence with cluster size by introducing a lattice self-energy with continuous momentum dependence. However, we show that the DCA + algorithm is plagued by a fundamental problem when its self-consistency equations are formulated using the bare Green's function of the cluster. This problem is most severe in the strongly correlated regime at low doping, where the DCA + self-energy becomes overly metallic and local, and persists to cluster sizes where the standard DCA has long converged. In view of the failure of the DCA + algorithm, we propose to complement DCA simulations with a post-interpolation procedure for single-particle and two-particle correlation functions to preserve continuous momentum dependence and the associated benefits in the DCA. We demonstrate the effectiveness of this practical approach with results for the half-filled and hole-doped two-dimensional Hubbard model.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Testing higher-order Lagrangian perturbation theory against numerical simulation. 1: Pancake models

We present results showing an improvement of the accuracy of perturbation theory as applied to cosmological structure formation for a useful range of quasi-linear scales. The Lagrangian theory of gravitational instability of an Einstein-de Sitter dust cosmogony investigated and solved up to the third order is compared with numerical simulations. In this paper we study the dynamics of pancake models as a first step. In previous work the accuracy of several analytical approximations for the modeling of large-scale structure in the mildly non-linear regime was analyzed in the same way, allowing for direct comparison of the accuracy of various approximations. In particular, the Zel'dovich approximation (hereafter ZA) as a subclass of the first-order Lagrangian perturbation solutions was found to provide an excellent approximation to the density field in the mildly non-linear regime (i.e. up to a linear r.m.s. density contrast of sigma is approximately 2). The performance of ZA in hierarchical clustering models can be greatly improved by truncating the initial power spectrum (smoothing the initial data). We here explore whether this approximation can be further improved with higher-order corrections in the displacement mapping from homogeneity. We study a single pancake model (truncated power-spectrum with power-spectrum with power-index n = -1) using cross-correlation statistics employed in previous work. We found that for all statistical methods used the higher-order corrections improve the results obtained for the first-order solution up to the stage when sigma (linear theory) is approximately 1. While this improvement can be seen for all spatial scales, later stages retain this feature only above a certain scale which is increasing with time. However, third-order is not much improvement over second-order at any stage. The total breakdown of the perturbation approach is observed at the stage, where sigma (linear theory) is approximately 2, which corresponds to the onset of hierarchical clustering. This success is found at a considerable higher non-linearity than is usual for perturbation theory. Whether a truncation of the initial power-spectrum in hierarchical models retains this improvement will be analyzed in a forthcoming work.

Buchert, T.↗

Identification of a Na + -Binding Site near the Oxygen-Evolving Complex of Spinach Photosystem II

The oxygen-evolving complex (OEC) of photosystem II (PSII) is an oxomanganese cluster composed of four redox-active Mn ions, and one redox-inactive Ca 2+ ion, with two nearby bound Cl – ions. Sodium is a common counter-ion of both chloride and hydroxide anions, and a sodium-specific binding site has not been identified near the OEC. Furthermore, we find that the oxygen-evolution activity of spinach PSII increases with [Na + ], particularly at high pH. A Na + -specific binding site next to the OEC, upon deprotonation of the D1-H337 amino-acid residue, is suggested by the analysis of two recently published PSII cryo-EM maps in combination with quantum mechanical calculations and molecular dynamics simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ion Conductivity and Correlations in Model Salt-Doped Polymers: Effects of Interaction Strength and Concentration

Correlated anion and cation motion can greatly reduce the overall ion conductivity in electrolytes versus the ideal conductivity calculated based on the diffusion constants alone. Using coarse-grained molecular dynamics simulations, we calculate conductivity and the degree of uncorrelated ion motion in salt-doped homopolymers and block copolymers as a function of concentration and interaction strengths. Calculating conductivity from ion mobility under an applied electric field increases accuracy versus the typical use of fluctuation dissipation relationships in equilibrium simulations. In typical electrolytes, correlation in cation-anion motion is often expected to be reduced at low ion concentrations. Yet, for these polymer electrolytes with strong ion-polymer and ion-ion interactions, we find cation-anion motion is more correlated at lower concentrations when other variables are held constant. We show this phenomenon is related to the slower ion cluster relaxation rate at low concentrations rather than the static spatial state of ion aggregation or the fraction of free ions.

36 MATERIALS SCIENCE↗

Ultrahigh-accuracy body-pointing system for the Large Space Telescope

The Large Space Telescope (LST) is a 3-m diffraction-limited telescope. Pointing stability requirements necessary to assure diffraction-limited images are plus or minus 0.005 arc-sec, over possible experiment observation times of several hours. In order to determine whether these stringent pointing requirements could be met, a complex simulation model was defined which consisted of detailed dynamic representations of control moment gyros (CMGs) and reaction wheels (RWs), including their noise characteristics, dynamic sensor representations with sensor noise, shock mounts for the CMG actuators, a detailed representation of an image motion compensation (IMC) system, and a detailed flexible body structural model with all significant vehicle and solar panel bending modes. On the basis of both stability and performance studies utilizing this model, it was determined that a body-pointing system will meet LST requirements in the presence of CMG vibrational disturbances and sensor noise. The recommended system consists of three orthogonally mounted RWs for primary short-term control, and a cluster of CMG actuators for continuous RW desaturation and vehicle maneuvering.

Rybak, S. C.↗

Integration of a Wigner effect-based energy storage system with an advanced nuclear reactor

In this work, an innovative energy storage concept based on the purposeful creation of defects in crystalline material by neutron irradiation is presented. Lattice defects are generated when heavy particles collide with the atoms in a crystal structure, i.e., if the incoming particles have enough energy, recoil atoms are displaced from their initial lattice sites. Most of the displaced atoms will eventually combine with nearby vacancies, but some of them will come to rest in non-ideal locations. The energy held by displaced atoms is called Wigner energy. Lattice defects can migrate and form clusters, and the Wigner energy can be released from these groupings if sufficient activation energy is provided. In the nuclear industry, this effect is well-known since it represented an issue for graphite-moderated reactors. This work presents the conceptual design of an engineering system that exploits this physical process to store the energy of neutrons in advanced reactor concepts. In the first part of the paper, the theoretical performance of an energy storage system based on the Wigner effect is described. Given the lattice properties and the compatibility with the harsh reactor environment, graphite was selected as the candidate material for the irradiation targets. Both experimental data and molecular dynamics simulations confirmed that this system can achieve performance comparable with state-of-the-art batteries in terms of stored energy density. In the second part of the paper, the engineering challenges of this innovative technology and the proposed solutions are described. After defining the optimal irradiation conditions, the different steps of the operation of the proposed energy system (from energy storing to energy harvesting) were defined. Finally, the integration of this concept with advanced reactor designs, i.e., a Sodium-cooled Fast Reactor and a Molten Salt-cooled Reactor, was investigated and the corresponding performance was evaluated.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Curvature-controlled geometrical lensing behavior in self-propelled colloidal particle systems

In many biological systems, the curvature of the surfaces cells live on influences their collective properties. Curvature should likewise influence the behavior of active colloidal particles. We show using molecular simulation of self-propelled active particles on surfaces of Gaussian curvature (both positive and negative) how curvature sign and magnitude can alter the system's collective behavior. Curvature acts as a geometrical lens and shifts the critical density of motility-induced phase separation (MIPS) to lower values for positive curvature and higher values for negative curvature, which we explain theoretically by the nature of parallel lines in spherical and hyperbolic space. Curvature also fluidizes dense MIPS clusters due to the emergence of defect patterns disrupting the crystalline order inside the clusters. Using our findings, we engineer three confining surfaces that strategically combine regions of different curvature to produce a host of novel dynamical behaviors, including cyclic MIPS on spherocylinders, directionally biased cyclic MIPS on spherocones, and position dependent cluster fluctuations on metaballs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Toward GEOS-6, A Global Cloud System Resolving Atmospheric Model

NASA is committed to observing and understanding the weather and climate of our home planet through the use of multi-scale modeling systems and space-based observations. Global climate models have evolved to take advantage of the influx of multi- and many-core computing technologies and the availability of large clusters of multi-core microprocessors. GEOS-6 is a next-generation cloud system resolving atmospheric model that will place NASA at the forefront of scientific exploration of our atmosphere and climate. Model simulations with GEOS-6 will produce a realistic representation of our atmosphere on the scale of typical satellite observations, bringing a visual comprehension of model results to a new level among the climate enthusiasts. In preparation for GEOS-6, the agency's flagship Earth System Modeling Framework [JDl] has been enhanced to support cutting-edge high-resolution global climate and weather simulations. Improvements include a cubed-sphere grid that exposes parallelism; a non-hydrostatic finite volume dynamical core, and algorithm designed for co-processor technologies, among others. GEOS-6 represents a fundamental advancement in the capability of global Earth system models. The ability to directly compare global simulations at the resolution of spaceborne satellite images will lead to algorithm improvements and better utilization of space-based observations within the GOES data assimilation system

Putman, William M.↗

Fluctuation dynamo in a weakly collisional plasma

The turbulent amplification of cosmic magnetic fields depends upon the material properties of the host plasma. In many hot, dilute astrophysical systems, such as the intracluster medium (ICM) of galaxy clusters, the rarity of particle–particle collisions allows departures from local thermodynamic equilibrium. These departures – pressure anisotropies – exert anisotropic viscous stresses on the plasma motions that inhibit their ability to stretch magnetic-field lines. We present an extensive numerical study of the fluctuation dynamo in a weakly collisional plasma using magnetohydrodynamic (MHD) equations endowed with a field-parallel viscous (Braginskii) stress. When the stress is limited to values consistent with a pressure anisotropy regulated by firehose and mirror instabilities, the Braginskii-MHD dynamo largely resembles its MHD counterpart, particularly when the magnetic field is dynamically weak. If instead the parallel viscous stress is left unabated – a situation relevant to recent kinetic simulations of the fluctuation dynamo and, we argue, to the early stages of the dynamo in a magnetized ICM – the dynamo changes its character, amplifying the magnetic field while exhibiting many characteristics reminiscent of the saturated state of the large-Prandtl-number ( ${Pm}\gtrsim {1}$ ) MHD dynamo. We construct an analytic model for the Braginskii-MHD dynamo in this regime, which successfully matches simulated dynamo growth rates and magnetic-energy spectra. A prediction of this model, confirmed by our numerical simulations, is that a Braginskii-MHD plasma without pressure-anisotropy limiters will not support a dynamo if the ratio of perpendicular and parallel viscosities is too small. This ratio reflects the relative allowed rates of field-line stretching and mixing, the latter of which promotes resistive dissipation of the magnetic field. Finally, in all cases that do exhibit a viable dynamo, the generated magnetic field is organized into folds that persist into the saturated state and bias the chaotic flow to acquire a scale-dependent spectral anisotropy.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Segmental Dynamics and Vitrification in Associating Copolymer Melts: Role of Cluster Formation, Microdomains, and Cross-Linking

A microscopic statistical mechanical theory of the structure, self-assembly, and activated segmental relaxation is employed to study associating copolymer melts with high attractive sticker fractions, local clustering, and disordered microphase ordering. The stickers are dynamically pinned in a manner that does not affect equilibrium structure which mimics the much slower physical bond breaking process or postassembly cross-linking of sticky monomers. Local sticker clustering and microdomain spatial correlations significantly modify the activated relaxation of nonstickers and glass transition temperature, T g . A re-entrant glass-melting feature is predicted as sticker attraction strength is initially increased corresponding to a speed up of segmental relaxation, and hence reduction of T g relative to the cross-linked homopolymer network. A mechanistic analysis reveals three competing effects: a purely kinetic slowing down of nonstickers down due to cross-linking, disordering of the nonsticker local cage and weakening of effective forces they experience due to sticker physical clustering, and a longer range impact of microdomain scale correlations that results in nonmonotonic dynamical effects. At high enough attraction strength, a qualitative change emerges corresponding to a sticker fraction dependent elevation of T g , which eventually surpasses that of the cross-linked homopolymer network. Dynamically, the new physics arises from a complex evolution of the amplitude of the collective elastic field that dresses the large amplitude mobile segment hopping within a coupled local-nonlocal description of the alpha relaxation. Furthermore, the results are qualitatively consistent with recent experiments on associating PDMS and PPG telechelics of fixed sticker fraction but with chemically different end groups of variable attraction strengths. Finally, possible tests using simulation and the influence of material or model specific interaction potentials and other real world complications are discussed.

Copolymers↗

Graphene-extracted membrane lipids facilitate the activation of integrin α v β 8

Despite the remarkable electrochemical properties of graphene, strong van der Waals attraction between graphene and biomolecules often causes cytotoxicity, which hinders its applications in the biomedical field. Unfortunately, surface passivation of graphene might stimulate undesired immune response as the nanomaterial triggers cytokine production through membrane receptor activation. In this work, we use all-atom Molecular Dynamics (MD) simulations to unravel the underlying mechanism of graphene-induced inside-out activation of integrin αvβ8, a prominent membrane receptor expressed in immune cells. We model the transmembrane (TM) domains of integrin αvβ8 in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer and observe the structural changes in the integrin–membrane complex when interacting with a graphene nanosheet across the membrane. We find that the β8 TM domain interacts with the graphene nanosheet directly or indirectly through extracted lipids, facilitating the pulling of a β8 subunit away from an αv subunit and thus leading to the disruption of the TM domain association by breaking the hydrophobic cluster in the cytoplasmic domains of the αv and β8 subunits. Alanine substitution of two conserved phenylalanine residues on the αv subunit at this hydrophobic cluster further reveals the importance of a stable T-shaped structure in retaining integrin in its inactive state. Our results agree with previous studies on the interactions between other integrin subtypes and their endogenous activators, suggesting an intriguing role that the graphene nanosheet may play in the integrin-related signal transduction during its interaction with the membrane.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Graphics Processing Unit (GPU) Acceleration of the Goddard Earth Observing System Atmospheric Model

The Goddard Earth Observing System 5 (GEOS-5) is the atmospheric model used by the Global Modeling and Assimilation Office (GMAO) for a variety of applications, from long-term climate prediction at relatively coarse resolution, to data assimilation and numerical weather prediction, to very high-resolution cloud-resolving simulations. GEOS-5 is being ported to a graphics processing unit (GPU) cluster at the NASA Center for Climate Simulation (NCCS). By utilizing GPU co-processor technology, we expect to increase the throughput of GEOS-5 by at least an order of magnitude, and accelerate the process of scientific exploration across all scales of global modeling, including: The large-scale, high-end application of non-hydrostatic, global, cloud-resolving modeling at 10- to I-kilometer (km) global resolutions Intermediate-resolution seasonal climate and weather prediction at 50- to 25-km on small clusters of GPUs Long-range, coarse-resolution climate modeling, enabled on a small box of GPUs for the individual researcher After being ported to the GPU cluster, the primary physics components and the dynamical core of GEOS-5 have demonstrated a potential speedup of 15-40 times over conventional processor cores. Performance improvements of this magnitude reduce the required scalability of 1-km, global, cloud-resolving models from an unfathomable 6 million cores to an attainable 200,000 GPU-enabled cores.

Putnam, Williama↗

The behavior of methane–water mixtures under elevated pressures from simulations using many-body potentials

Non-polarizable empirical potentials have been proven to be incapable of capturing the mixing of methane–water mixtures at elevated pressures. Although density functional theory-based ab initio simulations may circumvent this discrepancy, they are limited in terms of the relevant time and length scales associated with mixing phenomena. Here, we show that the many-body MB-nrg potential, designed to reproduce methane–water interactions with coupled cluster accuracy, successfully captures this phenomenon up to 3 GPa and 500 K with varying methane concentrations. Two-phase simulations and long time scales that are required to fully capture the mixing, affordable due to the speed and accuracy of the MBX software, are assessed. Constructing the methane–water equation of state across the phase diagram shows that the stable mixtures are denser than the sum of their parts at a given pressure and temperature. As a result, we find that many-body polarization plays a central role, enhancing the induced dipole moments of methane by 0.20 D during mixing under pressure. Overall, the mixed system adopts a denser state, which involves a significant enthalpic driving force as elucidated by a systematic many-body energy decomposition analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Intermolecular correlations of liquid and glassy CS 2 studied by synchrotron radiation x-ray diffraction

How is the orientation of molecular liquids ordered on cooling? What are the basic structures of molecular glasses, e.g., close to the crystalline structure or some special structures such as icosahedral cluster? These are long-standing questions in liquid and glass physics. Here, we have constructed a novel cryostat to prepare simple molecular glasses by vapor deposition and performed in situ synchrotron radiation x-ray diffraction experiments. The glassy state of a simple molecule CS 2 , which cannot be vitrified by normal liquid quenching, was successfully prepared with this instrument, and its diffraction data were collected in a wide Q-range of 0.16–25.7 Å -1 with a high-energy diffractometer at BL04B2, SPring-8. The diffraction data of liquid CS 2 were also recorded in a wide temperature range of 160–300 K. These diffraction data were analyzed with molecular dynamics simulations and reverse Monte Carlo modelings to investigate orientational correlation. From the obtained 3D structure models, the orientational correlation between neighboring CS 2 molecules was investigated quantitatively as a function of temperature. At room temperature, the parallel and T-shaped arrangements are preferred for the nearest neighbor correlation. On cooling, these arrangements are developed gradually, and its rate became prominent below the melting temperature (162 K). In the glassy state, the slipped-parallel arrangement is dominant as well as the T-shaped arrangement. Both arrangements appear in the CS 2 crystal, indicating that the structure of glassy CS 2 is close to that of crystalline CS 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Resolving Salt-Induced Agglomeration of Laponite Suspensions Using X-ray Photon Correlation Spectroscopy and Molecular Dynamics Simulations

Linking the physics of the relaxation behavior of viscoelastic fluids as they form arrested gel states to the underlying chemical changes is essential for developing predictive controls on the properties of the suspensions. In this study, 3 wt.% laponite suspensions are studied as model systems to probe the influence of salt-induced relaxation behavior arising from the assembly of laponite nanodisks. X-ray Photon Correlation Spectroscopy (XPCS) measurements show that laponite suspensions prepared in the presence of 5 mM concentrations of CaCl2, MgCl2 and CsCl salts accelerate the formation of arrested gel states, with CaCl2 having a significant impact followed by CsCl and MgCl2 salts. The competing effects of ion size and charge on relaxation behavior are noted. For example, the relaxation times of laponite suspensions in the presence of Mg2+ ions are slower compared to Cs+ ions despite the higher charge, suggesting that cation size dominates in this scenario. The faster relaxation behavior of laponite suspensions in the presence of Ca2+ ions compared to Cs+ ions shows that a higher charge dominates the size of the ion. The trends in relaxation behavior are consistent with the cluster formation behavior of laponite suspensions and the electrostatic interactions predicted from MD simulations. Charge balance is achieved by the intercalation of the cations at the negatively charged surfaces of laponite suspensions. These studies show that the arrested gel state of laponite suspensions is accelerated in the presence of salts, with ion sizes and charges having a competing effect on relaxation behavior.

36 MATERIALS SCIENCE↗

Shape-dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks

Development of characteristic tissue patterns requires that individual cells be switched locally between different phenotypes or "fates;" while one cell may proliferate, its neighbors may differentiate or die. Recent studies have revealed that local switching between these different gene programs is controlled through interplay between soluble growth factors, insoluble extracellular matrix molecules, and mechanical forces which produce cell shape distortion. Although the precise molecular basis remains unknown, shape-dependent control of cell growth and function appears to be mediated by tension-dependent changes in the actin cytoskeleton. However, the question remains: how can a generalized physical stimulus, such as cell distortion, activate the same set of genes and signaling proteins that are triggered by molecules which bind to specific cell surface receptors. In this article, we use computer simulations based on dynamic Boolean networks to show that the different cell fates that a particular cell can exhibit may represent a preprogrammed set of common end programs or "attractors" which self-organize within the cell's regulatory networks. In this type of dynamic network model of information processing, generalized stimuli (e.g., mechanical forces) and specific molecular cues elicit signals which follow different trajectories, but eventually converge onto one of a small set of common end programs (growth, quiescence, differentiation, apoptosis, etc.). In other words, if cells use this type of information processing system, then control of cell function would involve selection of preexisting (latent) behavioral modes of the cell, rather than instruction by specific binding molecules. Importantly, the results of the computer simulation closely mimic experimental data obtained with living endothelial cells. The major implication of this finding is that current methods used for analysis of cell function that rely on characterization of linear signaling pathways or clusters of genes with common activity profiles may overlook the most critical features of cellular information processing which normally determine how signal specificity is established and maintained in living cells. Copyright 2000 Academic Press.

Review↗

The Ionization History of The Intergalactic Medium:

The funded project seeked a unified description of the ionization, physical structure, and evolution of the intergalactic medium (IGM) and quasar intervening absorption systems. We proposed to conduct theoretical studies of the IGM and QSO absorbers in the context of current theories of galaxy formation, developing and using numerical and analytical techniques aimed at a detailed modeling of cosmological radiative transfer, gas dynamics, and thermal and ionization evolution. The ionization history of the IGM has important implications for the metagalactic UV background, intergalactic helium absorption 21-cm tomography, metal absorption systems, fluctuations in the microwave background, and the cosmic rate of structure and star formation. All the original objectives of our program have been achieved, and the results widely used and quoted by the community. Indeed, they remain relevant as the level and complexity of research in this area has increased substantially since our proposal was submitted, due to new discoveries on galaxy formation and evolution, a flood of high-quality data on the distant universe, new theoretical ideas and direct numerical simulations of structure formation in hierarchical clustering theories.

Madau, Piero↗

EMPDF : inferring the Milky Way mass with data-driven distribution function in phase space

We introduce the emPDF (empirical distribution function), a novel dynamical modelling method that infers the gravitational potential from kinematic tracers with optimal statistical efficiency under the minimal assumption of steady state. emPDF determines the best-fitting potential by maximizing the similarity between instantaneous kinematics and the time-averaged phase-space distribution function (DF), which is empirically constructed from observation upon the theoretical foundation of oPDF (Han et al. 2016). This approach eliminates the need for presumed functional forms of DFs or orbit libraries required by conventional DF- or orbit-based methods. emPDF stands out for its flexibility, efficiency, and capability in handling observational effects, making it preferable to the popular Jeans equation or other minimal assumption methods, especially for the Milky Way (MW) outer halo where tracers often have limited sample size and poor data quality. We apply emPDF to infer the MW mass profile using Gaia DR3 data of satellite galaxies and globular clusters, obtaining enclosed masses of M (,r) = 26±8, 46±8, 90±13⁠, and 149±40 x 10 10 M ⊙ at r = 30, 50, 100⁠, and 200 kpc, respectively. These are consistent with the updated constraints from simulation-informed DF fitting (Li et al. 2020). While the simulation-informed DF offers superior precision owing to the additional information extracted from simulations, emPDF is independent of such supplementary knowledge and applicable to general tracer populations. emPDF is currently implemented for tracers with complete 6D kinematics within spherical potentials, but it can potentially be extended to address more general problems.

Astrophysics of Galaxies (astro-ph.GA)↗