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At least 1,729 records · Page 96

Spontaneous emergence of autocatalytic information-coding polymers

Self-replicating systems based on information-coding polymers are of crucial importance in biology. They also recently emerged as a paradigm in material design on nano- and micro-scales. We present a general theoretical and numerical analysis of the problem of spontaneous emergence of autocatalysis for heteropolymers capable of template-assisted ligation driven by cyclic changes in the environment. Our central result is the existence of the first order transition between the regime dominated by free monomers and that with a self-sustaining population of sufficiently long chains. We provide a simple, mathematically tractable model supported by numerical simulations, which predicts the distribution of chain lengths and the onset of autocatalysis in terms of the overall monomer concentration and two fundamental rate constants. Another key result of our study is the emergence of the kinetically limited optimal overlap length between a template and each of its two substrates. The template-assisted ligation allows for heritable transmission of the information encoded in chain sequences thus opening up the possibility of long-term memory and evolvability in such systems.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Modeling of EAST ICRF antenna performance using the full-wave code TORIC

Access to advanced operating regimes in the EAST tokamak will require a combination of electron-cyclotron resonance heating (ECRH), neutral beam injection (NBI) and ion cyclotron range frequency heating (ICRF), with the addition of lower-hybrid current drive (LHCD) for current profile control. Prior experiments at the EAST tokamak facility have shown relatively weak response of the plasma temperature to application of ICRF heating, with typical coupled power about 2 MW out of 12 MW source. The launched spectrum, at n{sub φ} = 34 for 0-π -0-π phasing and 27 MHz, is largely inaccessible at line-averaged densities of approximately 2 × 10{sup 19} m{sup −3}. However, with variable antenna phasing and frequency, this system has considerable latitude to explore different heating schemes. To develop an ICRF actuator control model, we have used the full-wave code TORIC to explore the physics of ICRF wave propagation in EAST. The results presented from this study use a spectrum analysis using a superposition of n{sub φ} spanning −50 to +50. The low density regime typical of EAST plasmas results in a perpendicular wavelength comparable to the minor radius which results in global cavity resonance effects and eigenmode formation when the single-pass absorption is low. This behavior indicates that improved performance can be attained by lowering the peak of the k{sub ||} spectrum by using π/3 phasing of the 4-strap antenna. Based on prior studies conducted at Alcator C-Mod, this phasing is also expected to have the advantage of nearly divergence-free box currents, which should result in reduced levels of impurity production. Significant enhancements of the loading resistance may be achieved by using low k{sub ||} phasing and a combination of magnetic field and frequency to vary the location of the resonance and mode conversion regions. TORIC calculations indicate that the significant power may be channeled to the electrons and deuterium majority. We expect that implementation of these recommendations in EAST will yield substantial improvements in the net absorbed power that will greatly assist in the attempt to access advanced tokamak operating regimes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

New developments of the CARTE thermochemical code: A two-phase equation of state for nanocarbons

We developed a new equation of state (EOS) for nanocarbons in the thermodynamic range of high explosives detonation products (up to 50 GPa and 4000 K). This EOS was fitted to an extensive database of thermodynamic properties computed by molecular dynamics simulations of nanodiamonds and nano-onions with the LCBOPII potential. We reproduced the detonation properties of a variety of high explosives with the CARTE thermochemical code, including carbon-poor and carbon-rich explosives, with excellent accuracy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

On a stochastic approach to a code performance estimation

The main goal of an efficient profiling of software is to minimize the runtime overhead under certain constraints and requirements. The traces built by a profiler during the work, affect the performance of the system itself. One of important aspect of an overhead arises from the randomness of variability in the context in which the application is embedded, e.g., due to possible cache misses, etc. Such uncertainty needs to be taken into account in the design phase. In order to overcome these difficulties we propose to investigate this issue through the analysis of the probability distribution of the difference between profiler’s times for the same code. The approximating model is based on the finite normal mixtures within the framework of the method of moving separation of mixtures. We demonstrate some results for the MATLAB profiler using plotting of 3D surfaces by the function surf. The idea can be used for an estimating of a program efficiency.

97 MATHEMATICS AND COMPUTING↗

Alfvén ionization in an MHD-gas interactions code

A numerical model of partially ionized plasmas is developed in order to capture their evolving ionization fractions as a result of Alfvén ionization (AI). The mechanism of, and the parameter regime necessary for, AI is discussed and an expression for the AI rate based on fluid parameters, from a gas-MHD model, is derived. This AI term is added to an existing MHD-gas interactions' code, and the result is a linear, 2D, two-fluid model that includes momentum transfer between charged and neutral species as well as an ionization rate that depends on the velocity fields of both fluids. The dynamics of waves propagating through such a partially ionized plasma are investigated, and it is found that AI has a significant influence on the fluid dynamics as well as both the local and global ionization fraction.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Verification of long wavelength electromagnetic modes with a gyrokinetic-fluid hybrid model in the XGC code

As an alternative option to kinetic electrons, the gyrokinetic total-f particle-in-cell (PIC) code XGC1 has been extended to the MHD/fluid type electromagnetic regime by combining gyrokinetic PIC ions with massless drift-fluid electrons. Here, two representative long wavelength modes, shear Alfven waves and resistive tearing modes, are verified in cylindrical and toroidal magnetic field geometries.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Extension of the SIESTA MHD equilibrium code to free-plasma-boundary problems

Here, SIESTA is a recently developed MHD equilibrium code designed to perform fast and accurate calculations of ideal MHD equilibria for three-dimensional magnetic configurations. Since SIESTA does not assume closed magnetic surfaces, the solution can exhibit magnetic islands and stochastic regions. In its original implementation SIESTA addressed only fixed-boundary problems. That is, the shape of the plasma edge, assumed to be a magnetic surface, was kept fixed as the solution iteratively converges to equilibrium. This condition somewhat restricts the possible applications of SIESTA. In this paper we discuss an extension that will enable SIESTA to address free-plasma-boundary problems, opening up the possibility of investigating problems in which the plasma boundary is perturbed either externally or internally. As an illustration, SIESTA is applied to a configuration of the W7-X stellarator.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Validation of extended magnetohydrodynamic simulations of the HIT-SI3 experiment using the NIMROD code

The HIT-SI3 experiment uses a set of inductively driven helicity injectors to apply a non-axisymmetric current drive on the edge of the plasma, driving an axisymmetric spheromak equilibrium in a central confinement volume. These helicity injectors drive a non-axisymmetric perturbation that oscillates in time, with relative temporal phasing of the injectors modifying the mode structure of the applied perturbation. A set of three experimental discharges with different perturbation spectra are modelled here using the NIMROD extended magnetohydrodynamics code, and comparisons are made to both magnetic and fluid measurements. These models successfully capture the bulk dynamics of both the perturbation and the equilibrium, though disagreements related to the pressure gradients experimentally measured exist.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A fast low-to-high confinement mode bifurcation dynamics in the boundary-plasma gyrokinetic code XGC1

Here, a fast edge turbulence suppression event has been simulated in the electrostatic version of the gyrokinetic particle-in-cell code XGC1 in a realistic diverted tokamak edge geometry under neutral particle recycling. The results show that the sequence of turbulent Reynolds stress followed by neoclassical ion orbit-loss driven together conspire to form the sustaining radial electric field shear and to quench turbulent transport just inside the last closed magnetic flux surface. As a result, the main suppression action is located in a thin radial layer around ψ N ≃0.96–0.98, where ψ N is the normalized poloidal flux, with the time scale ~0.1 ms.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Radial transport modeling of high density deuterium plasmas in proto-MPEX with the B2.5-Eirene code

High density (≥6 × 10 19 m –3 ), low temperature (2–6 eV) helicon discharges in the Prototype Material Plasma Exposure eXperiment (Proto-MPEX) are analyzed with the coupled multifluid plasma, kinetic neutrals code B2.5-Eirene. The interpretative analyses are constrained by data from multiple diagnostics, including Langmuir probes, Mach probes, filterscopes, infrared TV system, Thomson scattering, and baratrons. The objectives of the transport simulations include: investigation of the effects of heating, fueling, and plasma production; pumping, and assumed radial transport models on the calculated density and temperature distributions; plasma flow profiles and power balance. The primary objective in this report is to investigate the effects of the radial transport model in full plasma (the entire length of the plasma column in Proto-MPEX) data-constrained simulations. Results from three assumed forms of the radial transport coefficients are presented, including spatially constant, radially decreasing, and Bohm (D,χ ~T e /|B|). The results from each of the three transport coefficient sets agree qualitatively with the core (near axis) data. With the implicit T e dependence, the Bohm coefficients tend to decrease as functions of radius, although not as strongly as the centrally peaked set. The axial variation in the Bohm coefficients is largely due to the axial structure of the magnetic field. Furthermore, the agreement of the simulations and the diagnostic data with the Bohm set indicates that transport in the plasma column of Proto-MPEX is dominated by Bohm diffusion.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Examination of synthetic gas puff imaging diagnostic data from a gyrokinetic turbulence code

A synthetic gas puff imaging (GPI) diagnostic has been developed for the purpose of validating the three-dimensional gyrokinetic turbulence code XGC. The synthetic diagnostic is described and applied to XGC simulations of two Alcator C-Mod discharges. The turbulence characteristics deduced from the resulting simulated GPI frames, using analysis techniques similar to those applied to experimental data, are compared with locally derived characteristics extracted directly from the XGC output. The comparison of the two is shown to be potentially impacted by misalignment between the GPI view and the magnetic field, the dependence of the light emission on the electron density and temperature, and spatial and temporal variations in the neutral gas cloud induced by the turbulent plasma fluctuations. We conclude that quantitative and, in some cases even qualitative, validation of turbulence simulations need to account for these effects. While we cannot directly compare our results with experimental data due to the absence of high quality GPI data from the shots and times simulated by XGC, we do relate the overall characteristics obtained from the synthetic GPI analysis to published Alcator C-Mod GPI data.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Spatial core-edge coupling of the particle-in-cell gyrokinetic codes GEM and XGC

Two existing particle-in-cell gyrokinetic codes, GEM for the core region and XGC for the edge region, have been successfully coupled with a spatial coupling scheme at the interface in a toroidal geometry. Additionally, a mapping technique is developed for transferring data between GEM's structured and XGC's unstructured meshes. Two examples of coupled simulations are presented to demonstrate the coupling scheme. The optimization of GEM for graphics processing unit is also presented.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Property of neoclassical GAMs induced by pellet generated plasma perturbations in the gyrokinetic code XGC

A pellet source model has been implemented into the gyrokinetic code XGC and applied to neoclassical geodesic acoustic mode (GAM) study as the first step to investigate potentially rapid kinetic spread of pellet-born particles following their injection into plasma. Here in this study, GAM oscillations of the radial electric field, as well as of their effect on the radial particle and energy fluxes, are studied and the observed frequencies agree with theoretical expectations. It is verified that (i) GAM oscillations are driven both within the pellet-fuelled region and for locations at a larger radius than this region and not for locations radially inside the pellet-fuelled region, and that, (ii) even though the poloidal spread along the magnetic field lines is fast, the time-averaged radial plasma transport under GAM oscillations is kept to roughly the same level as the neoclassical transport in the absence of plasma turbulence.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Single-shot x-ray phase-contrast and dark-field imaging based on coded binary phase mask

We introduce a coded-mask-based multi-contrast imaging method for high-resolution phase-contrast and dark-field imaging. The method uses a binary phase mask designed to provide an ultra-high-contrast pattern and reference-free single-shot measurement and an algorithm based on maximum-likelihood optimization and automatic differentiation to perform simultaneous reconstruction of absorption, phase, and dark-field object images. Further, we demonstrate that the method has great potential for real-time quantitative phase imaging and wavefront sensing when combined with deep learning.

Qiao, Zhi (ORCID:0000000286285320)↗

ATEQ: Adaptive toroidal equilibrium code

A radially adaptive numerical scheme is developed to solve the Grad–Shafranov equation for axisymmetric magnetohydrodynamic equilibrium. Here, a decomposition with independent solutions is employed in the radial direction, and Fourier decomposition is used in the poloidal direction. The independent solutions are then obtained using an adaptive shooting scheme together with the multi-region matching technique in the radial direction. Accordingly, the adaptive toroidal equilibrium (ATEQ) code is constructed for axisymmetric equilibrium studies. The adaptive numerical scheme in the radial direction improves considerably the accuracy of the equilibrium solution. The decomposition with independent solutions effectively reduces the matrix size in solving the magnetohydrodynamic equilibrium problem. The reduction of the matrix size is about an order of magnitude as compared with the conventional radially grid-based numerical schemes. Also, in this ATEQ numerical scheme, no matter how accuracy in the radial direction is imposed, the size of matrices basically does not change. The small matrix size scheme gives ATEQ more flexibility to address the requirement of the number of Fourier components in the poloidal direction in tough equilibrium problems. These two unique features, the adaptive shooting and small matrix size, make ATEQ useful to improve tokamak equilibrium solutions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Implementing Faraday effect measurement constraints into the Grad–Shafranov equilibrium fitting code EFIT

A new tool for the exploration and diagnosis of the internal magnetic field of plasmas in the DIII-D tokamak in the form of a constraint on the EFIT (Equilibrium Fitting) Grad–Shafranov code based on the Faraday-effect Radial Interferometer-Polarimeter (RIP) diagnostic is presented, including description, verification, and sample application. The physics underlying the diagnostic and its implementation into EFIT are discussed, and the results showing the verification of the model are given, and the model’s limitations are discussed. The influence of the diagnostic’s input on the resulting equilibrium parameters is characterized. Furthermore, the effect of electron density profile refinement is evaluated and found to be negligible. A sample application of the diagnostic is shown, indicating that the RIP constraint has similar effects on the equilibrium as motional Stark effect constraints do.

47 OTHER INSTRUMENTATION↗

Nonlinear models for coupling the effects of stimulated Raman scattering to inertial confinement fusion codes

Laser plasma instabilities (LPI) reduce driver-target coupling, alter implosion symmetry, and therefore can fundamentally limit fusion performance in inertial confinement fusion (ICF). Developing a predictive modeling capability for LPI effects can critically advance the success of the field. We perform vector particle-in-cell simulations of multi-speckled laser beams undergoing stimulated Raman scattering (SRS) at various densities and intensities relevant to mainly indirectly driven and a subset of parameter space for directly driven ICF systems, focusing on the regimes with intensities above the onset of electron trapping. Based on the wavenumber of the SRS daughter electron plasma wave, we identify several regions with underpinning SRS saturation physics: the electron-trapping dominated region with intermediate kλD values, the strong Landau damping region at larger kλD values, and the region where the Langmuir decay instability arises at lower kλD values. We develop a nonlinear SRS reflectivity model that features the base trapping-dominated scaling of (kλD)−4 and its modifications. Electron trapping deforms the initialized electron distribution functions, and we have developed a new δf-Gaussian-mixture algorithm for an accurate characterization of the trapped hot electron population. With this SRS hot electron description, we construct a nonlinear energy deposition model and a hot electron source model—based on a modified Manley–Rowe relation—suitable for including SRS effects as a sub-grid module in a high-fidelity ICF design code.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

GPU acceleration of local and semilocal density functional calculations in the SPARC electronic structure code

We present a Graphics Processing Unit (GPU)-accelerated version of the real-space SPARC electronic structure code for performing Kohn–Sham density functional theory calculations within the local density and generalized gradient approximations. In particular, we develop a modular math-kernel based implementation for NVIDIA architectures wherein the computationally expensive operations are carried out on the GPUs, with the remainder of the workload retained on the central processing units (CPUs). Here, using representative bulk and slab examples, we show that relative to CPU-only execution, GPUs enable speedups of up to 6× and 60× in node and core hours, respectively, bringing time to solution down to less than 30 s for a metallic system with over 14 000 electrons and enabling significant reductions in computational resources required for a given wall time.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗