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At least 595 records · Page 33

On the implementation of the spherical collapse model for dark energy models

In this work we review the theory of the spherical collapse model and critically analyse the aspects of the numerical implementation of its fundamental equations. By extending a recent work by [1], we show how different aspects, such as the initial integration time, the definition of constant infinity and the criterion for the extrapolation method (how close the inverse of the overdensity has to be to zero at the collapse time) can lead to an erroneous estimation (a few per mill error which translates to a few percent in the mass function) of the key quantity in the spherical collapse model: the linear critical overdensity δ{sub c}, which plays a crucial role for the mass function of halos. We provide a better recipe to adopt in designing a code suitable to a generic smooth dark energy model and we compare our numerical results with analytic predictions for the EdS and the ΛCDM models. We further discuss the evolution of δ{sub c} for selected classes of dark energy models as a general test of the robustness of our implementation. We finally outline which modifications need to be taken into account to extend the code to more general classes of models, such as clustering dark energy models and non-minimally coupled models.

79 ASTRONOMY AND ASTROPHYSICS↗

A new implementation of dynamic polarizability evaluation using a multi-resolution multi-wavelet basis set

An algorithm to evaluate the response function on the space spanned by Multiresolution Multi-wavelet (MRMW) basis functions is implemented in a new efficient quantum chemical program system. Dynamic electric dipole polarizability of a molecule is evaluated for a range of applied optical frequencies as a preliminary application of the implementation. The results obtained by the MRMW provide the one in near completeness limit. We also compare a few examples of the dynamic polarizabilities evaluated using conventional Gaussian basis set functions with the one evaluated by the MMMW basis functions. For small frequencies, there is no significant difference among them and large Gaussian results are close to the MRMW value, but they diverge from the MRMW value when the applied frequency approaches to the resonance region.

74 ATOMIC AND MOLECULAR PHYSICS↗

The implementation of Global Feature EXtractor (gFEX) - the ATLAS Calorimeter Level 1 Trigger system for LHC Run-3 upgrade

As part of the ATLAS Phase-I Upgrade, the global Feature EXtractor (gFEX) is one of several hardware modules designed to help maintain the ATLAS Level-1 trigger acceptance rate with the increasing Large Hadron Collider (LHC) luminosity and the increasing Pile-Up conditions. The gFEX is used to identify patterns of energy associated with the hadronic decays of high momentum Higgs, W & Z bosons, top quarks, and exotic particles in real time at the 40 MHz LHC bunch crossing rate. The board is required to receive coarse-granularity (Δη×Δphiv = 0.2×0.2 gTower) information from the entire ATLAS calorimeters on 276 optical fibers. A prototype v1 with one Xilinx ZYNQ FPGA, and one Vertex-7 FPGA for technology validation has been designed and tested in 2015. With the lessons learned from the prototype v1, a prototype v2 with three Vertex UltraScale FPGAs and one ZYNQ FPGA has been implemented to verify full functionalities of gFEX in 2016. Based on the prototype v2 design, a prototype v3, the final gFEX prototype, is implemented, which is an ATCA module consisting of three Vertex UltraScale+ FPGAs, one ZYNQ UltraScale+ SoC, and 35 MiniPODs. This board receives up to 300 fiber optical links from calorimeters and transmits trigger data on 96 links to the to the ATLAS Level-1 Topological trigger (L1Topo [1]) at the speed up to 12.8 Gb/s. There are also 24 electrical links on board for communication between two FPGAs with the speed up to 25.6 Gb/s. The performance of three prototype boards have been tested and evaluated. For the prototype v3 board, the high-speed optical links are stable at 12.8 Gb/s with Bit Error Ratio (BER) < 1 × 10 -15 . The low-latency parallel GPIO (General Purpose I/O) buses between FPGAs are stable at 1.12 Gb/s. The peripheral components of ZYNQ UltraScale+ SoC, such as 16 GB DDR4 DIMM, UART, SPI flashes, and Ethernet, have also been verified. Here, the test results of the prototype v3 board validate the gFEX technologies, architecture and full functionalities. Now the final production board is being produced.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Seeing the forest for the trees: implementing dynamic representation of forest management and forest carbon in a long-term global multisector model

Abstract Studies have found that understanding forest management is critical in understanding the interaction between the carbon cycle and the integrated human-Earth system. This makes effectively representing forest management decisions such as planting and harvesting important. Here, we implement a novel dynamic forest harvest model in a global state of the art multi-sector dynamics model, namely the Global Change Analysis Model (GCAM). We implement an approach that explicitly tracks forest age and generates rotation ages for forest harvest that are responsive to changes in wood prices, changes in forest age and regional preferences for forest rotation. Furthermore, the forest sector in GCAM competes for investment with other land use types in the future years based on expected profit. Our baseline scenario results indicate that with the new forest harvest model, the current global wood product demand in GCAM can be met with minimal loss of old growth forest through the age-based harvest decisions. We find that economic pressure for deforestation and consequent loss of forest carbon is a bigger driver of global forest change than wood harvests, especially in developing regions. Under alternative scenarios where an economic value is placed on carbon across the terrestrial and energy systems, while there is an increase in forest plantations, there can be corresponding decreases in forest cover in some regions as forest land competes with land for bio-energy crops. When the carbon in forests is assigned a price, we find that the average rotation age for wood harvests can be reduced across regions to harvest forests in a more carbon efficient manner.

54 ENVIRONMENTAL SCIENCES↗

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit

Abstract Summary Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a practical MCMC method in the open-source software package PyBioNetFit (PyBNF), which is designed to support parameterization of mathematical models for biological systems. The new MCMC method, am, incorporates an adaptive move proposal distribution. For warm starts, sampling can be initiated at a specified location in parameter space and with a multivariate Gaussian proposal distribution defined initially by a specified covariance matrix. Multiple chains can be generated in parallel using a computer cluster. We demonstrate that am can be used to successfully solve real-world Bayesian inference problems, including forecasting of new Coronavirus Disease 2019 case detection with Bayesian quantification of forecast uncertainty. Availability and implementation PyBNF version 1.1.9, the first stable release with am, is available at PyPI and can be installed using the pip package-management system on platforms that have a working installation of Python 3. PyBNF relies on libRoadRunner and BioNetGen for simulations (e.g. numerical integration of ordinary differential equations defined in SBML or BNGL files) and Dask.Distributed for task scheduling on Linux computer clusters. The Python source code can be freely downloaded/cloned from GitHub and used and modified under terms of the BSD-3 license (https://github.com/lanl/pybnf). Online documentation covering installation/usage is available (https://pybnf.readthedocs.io/en/latest/). A tutorial video is available on YouTube (https://www.youtube.com/watch?v=2aRqpqFOiS4&t=63s). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Conserved unique peptide patterns (CUPP) online platform 2.0: implementation of +1000 JGI fungal genomes

Carbohydrate-processing enzymes, CAZymes, are classified into families based on sequence and three-dimensional fold. Because many CAZyme families contain members of diverse molecular function (different EC-numbers), sophisticated tools are required to further delineate these enzymes. Such delineation is provided by the peptide-based clustering method CUPP, Conserved Unique Peptide Patterns. CUPP operates synergistically with the CAZy family/subfamily categorizations to allow systematic exploration of CAZymes by defining small protein groups with shared sequence motifs. The updated CUPP library contains 21,930 of such motif groups including 3,842,628 proteins. The new implementation of the CUPP-webserver, https://cupp.info/, now includes all published fungal and algal genomes from the Joint Genome Institute (JGI), genome resources MycoCosm and PhycoCosm, dynamically subdivided into motif groups of CAZymes. This allows users to browse the JGI portals for specific predicted functions or specific protein families from genome sequences. Thus, a genome can be searched for proteins having specific characteristics. All JGI proteins have a hyperlink to a summary page which links to the predicted gene splicing including which regions have RNA support. The new CUPP implementation also includes an update of the annotation algorithm that uses only a fourth of the RAM while enabling multi-threading, providing an annotation speed below 1 ms/protein.

59 BASIC BIOLOGICAL SCIENCES↗

Implementation of two-party protocols in the noisy-storage model

The noisy-storage model allows the implementation of secure two-party protocols under the sole assumption that no large-scale reliable quantum storage is available to the cheating party. No quantum storage is thereby required for the honest parties. Examples of such protocols include bit commitment, oblivious transfer, and secure identification. Here, we provide a guideline for the practical implementation of such protocols. In particular, we analyze security in a practical setting where the honest parties themselves are unable to perform perfect operations and need to deal with practical problems such as errors during transmission and detector inefficiencies. We provide explicit security parameters for two different experimental setups using weak coherent, and parametric down-conversion sources. In addition, we analyze a modification of the protocols based on decoy states.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Implementation of the time-dependent configuration-interaction singles method for atomic strong-field processes

We present an implementation of the time-dependent configuration-interaction singles (TDCIS) method for treating atomic strong-field processes. In order to absorb the photoelectron wave packet when it reaches the end of the spatial grid, we add to the exact nonrelativistic many-electron Hamiltonian a radial complex absorbing potential (CAP). We determine the orbitals for the TDCIS calculation by diagonalizing the sum of the Fock operator and the CAP using a flexible pseudospectral grid for the radial degree of freedom and spherical harmonics for the angular degrees of freedom. The CAP is chosen such that the occupied orbitals in the Hartree-Fock ground state remain unaffected. Within TDCIS, the many-electron wave packet is expanded in terms of the Hartree-Fock ground state and its single excitations. The virtual orbitals satisfy nonstandard orthogonality relations, which must be taken into consideration in the calculation of the dipole and Coulomb matrix elements required for the TDCIS equations of motion. We employ a stable propagation scheme derived by second-order finite differencing of the TDCIS equations of motion in the interaction picture and subsequent transformation to the Schroedinger picture. Using the TDCIS wave packet, we calculate the expectation value of the dipole acceleration and the reduced density matrix of the residual ion. The technique implemented will allow one to study electronic channel-coupling effects in strong-field processes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Implementing quantum gates through scattering between a static and a flying qubit

We investigate whether a two-qubit quantum gate can be implemented in a scattering process involving a flying and a static qubit. To this end, we focus on a paradigmatic setup made out of a mobile particle and a quantum impurity, whose respective spin degrees of freedom couple to each other during a one-dimensional scattering process. Once a condition for the occurrence of quantum gates is derived in terms of spin-dependent transmission coefficients, we show that this can be actually fulfilled through the insertion of an additional narrow potential barrier. An interesting observation is that under resonance conditions this procedure enables a gate only for isotropic Heisenberg (exchange) interactions and fails for an XY interaction. We show the existence of parameter regimes for which gates able to establish a maximum amount of entanglement can be implemented. The gates are found to be robust to variations of the optimal parameters.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Entanglement requirements for implementing bipartite unitary operations

We prove, using a method based on map-state duality, lower bounds on entanglement resources needed to deterministically implement a bipartite unitary using separable (SEP) operations, which include LOCC (local operations and classical communication) as a particular case. It is known that the Schmidt rank of an entangled pure state resource cannot be less than the Schmidt rank of the unitary. We prove that if these ranks are equal the resource must be uniformly (maximally) entangled: equal nonzero Schmidt coefficients. Higher rank resources can have less entanglement: we have found numerical examples of Schmidt rank 2 unitaries, which can be deterministically implemented, by either SEP or LOCC, using an entangled resource of two qutrits with less than one ebit of entanglement.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Self-force via m-mode regularization and 2+1D evolution: Foundations and a scalar-field implementation on Schwarzschild spacetime

To model the radiative evolution of extreme mass-ratio binary inspirals (a key target of the LISA mission), the community needs efficient methods for computation of the gravitational self-force (SF) on the Kerr spacetime. Here we further develop a practical 'm-mode regularization' scheme for SF calculations, and give the details of a first implementation. The key steps in the method are (i) removal of a singular part of the perturbation field with a suitable 'puncture' to leave a sufficiently regular residual within a finite worldtube surrounding the particle's worldline, (ii) decomposition in azimuthal (m) modes, (iii) numerical evolution of the m modes in 2+1D with a finite-difference scheme, and (iv) reconstruction of the SF from the mode sum. The method relies on a judicious choice of puncture, based on the Detweiler-Whiting decomposition. We give a working definition for the ''order'' of the puncture, and show how it determines the convergence rate of the m-mode sum. The dissipative piece of the SF displays an exponentially convergent mode sum, while the m-mode sum for the conservative piece converges with a power law. In the latter case, the individual modal contributions fall off at large m as m{sup -n} for even n and as m{sup -n+1} for odd n, where n is the puncture order. We describe an m-mode implementation with a 4th-order puncture to compute the scalar-field SF along circular geodesics on Schwarzschild. In a forthcoming companion paper we extend the calculation to the Kerr spacetime.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Implementing a microphysics model in hydrodynamic simulations to study the initial plasma formation in dielectric ablator materials for direct-drive implosions

A microphysics model to describe the photoionization and impact ionization processes in dielectric ablator materials like plastic has been implemented into the 1-D hydrodynamic code LILAC for planar and spherical targets. Currently, the initial plasma formation during the early stages of a laser drive are modeled in an ad hoc manner, until the formation of a critical surface. Implementation of the physics-based models predict higher values of electron density, electron temperature, and pressure than the ad hoc model. Moreover, the numerical predictions are consistent with previous experimental observations of the shinethrough mechanism in plastic ablators. For planar targets, a decompression of the rear end of the target was observed, that is similar to recent experiments. An application of this model is to understand the laser-imprint mechanism that is caused by nonuniform laser irradiation due to single beam speckle.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Toward a 2D Local Implementation of Quantum Low-Density Parity-Check Codes

Geometric locality is an important theoretical and practical factor for quantum low-density parity-check (qLDPC) codes that affects code performance and ease of physical realization. For device architectures restricted to two-dimensional (2D) local gates, naively implementing the high-rate codes suitable for low-overhead fault-tolerant quantum computing incurs prohibitive overhead. In this work, we present an error-correction protocol built on a bilayer architecture that aims to reduce operational overheads when restricted to 2D local gates by measuring some generators less frequently than others. We investigate the family of bivariate-bicycle qLDPC codes and show that they are well suited for a parallel syndrome-measurement scheme using fast routing with local operations and classical communication (LOCC). Through circuit-level simulations, we find that in some parameter regimes, bivariate-bicycle codes implemented with this protocol have logical error rates comparable to the surface code while using fewer physical qubits. Published by the American Physical Society 2025

Berthusen, Noah (ORCID:0000000275862786)↗

Implementation of a self-consistent slab model of bilayer structure in the SasView suite

Slab models are simple and useful structural descriptions which have long been used to describe lyotropic lamellar phases, such as lipid bilayers. Typically, slab models assume a midline symmetry and break a bilayer structure into three pieces, a central solvent-free core and two symmetric outer layers composed of the soluble portion of the amphiphile and associated solvent. This breakdown matches reasonably well to the distribution of neutron scattering length density and therefore is a convenient and common approach for the treatment of small-angle scattering data. Here, an implementation of this model within the SasView software suite is reported. The implementation is intended to provide physical consistency through the area per amphiphile molecule and number of solvent molecules included within the solvent-exposed outer layer. The proper use of this model requires knowledge of (or good estimates for) the amphiphile and solvent molecule volume and atomic composition, ultimately providing a self-consistent data treatment with only two free parameters: the lateral area per amphiphile molecule and the number of solvent molecules included in the outer region per amphiphile molecule. Here, the use of this code is demonstrated in the fitting of standard lipid bilayer data sets, obtaining structural parameters consistent with prior literature and illustrating the typical and ideal cases of fitting for neutron scattering data obtained using single or multiple contrast conditions. While demonstrated here for lipid bilayers, this model is intended for general application to block copolymers, surfactants, and other lyotropic lamellar phase structures for which a slab model is able to reasonably estimate the neutron scattering length density/electron-density profile of inner and outer layers of the lamellae.

36 MATERIALS SCIENCE↗

Robust framework and software implementation for fast speciation mapping

One of the greatest benefits of synchrotron radiation is the ability to perform chemical speciation analysis through X-ray absorption spectroscopies (XAS). XAS imaging of large sample areas can be performed with either full-field or raster-scanning modalities. A common practice to reduce acquisition time while decreasing dose and/or increasing spatial resolution is to compare X-ray fluorescence images collected at a few diagnostic energies. In this work, several authors have used different multivariate data processing strategies to establish speciation maps. Furthermore, the theoretical aspects and assumptions that are often made in the analysis of these datasets are focused on. A robust framework is developed to perform speciation mapping in large bulk samples at high spatial resolution by comparison with known references. Two fully operational software implementations are provided: a user-friendly implementation within the MicroAnalysis Toolkit software, and a dedicated script developed under the R environment. The procedure is exemplified through the study of a cross section of a typical fossil specimen. Additionally, the algorithm provides accurate speciation and concentration mapping while decreasing the data collection time by typically two or three orders of magnitude compared with the collection of whole spectra at each pixel. Whereas acquisition of spectral datacubes on large areas leads to very high irradiation times and doses, which can considerably lengthen experiments and generate significant alteration of radiation-sensitive materials, this sparse excitation energy procedure brings the total irradiation dose greatly below radiation damage thresholds identified in previous studies. This approach is particularly adapted to the chemical study of heterogeneous radiation-sensitive samples encountered in environmental, material, and life sciences.

47 OTHER INSTRUMENTATION↗

Comparison of Conservation Behavior in Several Variationally Derived Implementations for Simulating Electromagnetic Plasmas

Variational techniques based on Low's Lagrangian formulation have demonstrated significant improvement in conservation properties as compared to traditional particle-in-cell (PIC) algorithms. Previous work showed that equations derived from a discretized Lagrangian preserve a discretized version of the connection between Lagrangian symmetries and conservation laws, i.e., Noether's theorem. Specifically, a thorough analysis of energy conservation within the new system explained the absence of “grid heating” phenomena. In the present work, variationally derived implementations in a gridded periodic domain were compared to analogous implementations using Fourier bases. Since the Fourier basis allows for exact momentum conservation, this approach enables us to compare the relative merits of exact and approximate momentum conservation. Furthermore, to establish a tangible comparison for numerical methods, we investigate two simple physical examples; (1) the coupling of an electrostatic and electromagnetic plasma wave and (2) an equilibrium supporting Weibel instability.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Design and Implementation of an optimized 100 kW stationary wireless charging system for EV battery recharging

This paper presents the design, analyses and implementation of an optimized single stage high power wireless charging system capable of transferring 100 kW at an operating frequency of 22 kHz and a coil-to-coil distance of 5 inches.The detailed design and implementation of the power electronics including the high frequency inverter and rectifier and wireless power transfer coils along with the resonant stage are described. FEA simulation results of the coils and the resonant network analysis are validated by using a Venable frequency response analyzer. Experimental results corresponding to 50 kW operation are presented to validate the design process.

Galigekere, Veda Prakash↗

Hyperparameter Optimization and Feature Inclusion in Graph Neural Networks for Spiking Implementation

Graph convolutional networks leverage both graph structures and features on nodes and edges for improved learning performance in comparison with classical machine learning approaches. Spiking neuromorphic computers natively implement network-like computation and have been shown to be successful at implementing graph learning without features. Incorporating graph features brings the challenge of efficient feature representation and balancing the contribution of topology and features in learning. In this work, we present our design of a simulated network of spiking neurons to perform semi-supervised learning on graph data using both the graph structure and the node features. We explore various design choices, present preliminary results, and discuss the opportunities for using neuromorphic computers for this task in the future.

Cong, Guojing↗