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At least 1,315 records · Page 73

Stochastic genetic networks with solvable structures

We describe a set of basic stochastic biocircuits for which the Master Equation is completely solvable. Beside linear circuits, which are known to be solvable, we show that tree-like circuits with polynomial transition functions are also completely solvable. We associate a simple but unambiguous graphical representation to such circuits. The graphical representation shows the signal propagation through these simple circuits.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Stability of an elliptical vortex in a strongly coupled dusty plasma

The stability of a long scale equilibrium vortex structure to short scale perturbations is studied in a strongly coupled dusty plasma in the framework of a generalized hydrodynamic model. It is shown that the free energy associated with the velocity shear of the vortex can drive secondary instabilities consisting of transverse shear waves when the resonance condition between the vortex rotation frequency and the secondary wave frequency is met. Such a process can transfer energy from the long scale vortex to the short scale secondary wave and thereby provide a saturation mechanism for long scale vortices in plasmas in a manner analogous to that in neutral fluids.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Parallel database search and prime factorization with magnonic holographic memory devices

In this work, we describe the capabilities of Magnonic Holographic Memory (MHM) for parallel database search and prime factorization. MHM is a type of holographic device, which utilizes spin waves for data transfer and processing. Its operation is based on the correlation between the phases and the amplitudes of the input spin waves and the output inductive voltage. The input of MHM is provided by the phased array of spin wave generating elements allowing the producing of phase patterns of an arbitrary form. The latter makes it possible to code logic states into the phases of propagating waves and exploit wave superposition for parallel data processing. We present the results of numerical modeling illustrating parallel database search and prime factorization. The results of numerical simulations on the database search are in agreement with the available experimental data. The use of classical wave interference may results in a significant speedup over the conventional digital logic circuits in special task data processing (e.g., √n in database search). Potentially, magnonic holographic devices can be implemented as complementary logic units to digital processors. Physical limitations and technological constrains of the spin wave approach are also discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Real-time data-intensive computing

Today users visit synchrotrons as sources of understanding and discovery—not as sources of just light, and not as sources of data. To achieve this, the synchrotron facilities frequently provide not just light but often the entire end station and increasingly, advanced computational facilities that can reduce terabytes of data into a form that can reveal a new key insight. The Advanced Light Source (ALS) has partnered with high performance computing, fast networking, and applied mathematics groups to create a “super-facility”, giving users simultaneous access to the experimental, computational, and algorithmic resources to make this possible. This combination forms an efficient closed loop, where data—despite its high rate and volume—is transferred and processed immediately and automatically on appropriate computing resources, and results are extracted, visualized, and presented to users or to the experimental control system, both to provide immediate insight and to guide decisions about subsequent experiments during beamtime. We will describe our work at the ALS ptychography, scattering, micro-diffraction, and micro-tomography beamlines.

43 PARTICLE ACCELERATORS↗

Wavelength-selective thermal extraction for higher efficiency and power density thermophotovoltaics

Thermophotovoltaics have long been of interest as an energy conversion technology but suffer from low power density and low efficiency. Structured emitters designed to alter the emission spectrum and increase the efficiency are not stable at the necessary high emitter temperatures and also reduce the power density. Here, we propose a wavelength-selective thermal extraction device that mitigates these challenges and demonstrate a transfer-printing process needed to fabricate the device. The device consists of a ZnS solid hemisphere with a patterned thin film optical filter that passively increases the far-field radiated flux from an emitter within a wavelength band near the bandgap of a photovoltaic cell. Crucially, the device does not need to be in physical contact with the emitter and thus can be maintained at a lower temperature, circumventing the thermal stability challenge. Our work helps one to address long-standing issues with applications of thermophotovoltaics.

14 SOLAR ENERGY↗

Quantum networks based on color centers in diamond

With the ability to transfer and process quantum information, large-scale quantum networks will enable a suite of fundamentally new applications, from quantum communications to distributed sensing, metrology, and computing. This Perspective reviews requirements for quantum network nodes and color centers in diamond as suitable node candidates. We give a brief overview of state-of-the-art quantum network experiments employing color centers in diamond and discuss future research directions, focusing, in particular, on the control and coherence of qubits that distribute and store entangled states, and on efficient spin–photon interfaces. We discuss a route toward large-scale integrated devices combining color centers in diamond with other photonic materials and give an outlook toward realistic future quantum network protocol implementations and applications.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A HYDROCHEMICAL HYBRID CODE FOR ASTROPHYSICAL PROBLEMS. I. CODE VERIFICATION AND BENCHMARKS FOR A PHOTON-DOMINATED REGION (PDR)

A two-dimensional hydrochemical hybrid code, KM2, is constructed to deal with astrophysical problems that would require coupled hydrodynamical and chemical evolution. The code assumes axisymmetry in a cylindrical coordinate system and consists of two modules: a hydrodynamics module and a chemistry module. The hydrodynamics module solves hydrodynamics using a Godunov-type finite volume scheme and treats included chemical species as passively advected scalars. The chemistry module implicitly solves nonequilibrium chemistry and change of energy due to thermal processes with transfer of external ultraviolet radiation. Self-shielding effects on photodissociation of CO and H{sub 2} are included. In this introductory paper, the adopted numerical method is presented, along with code verifications using the hydrodynamics module and a benchmark on the chemistry module with reactions specific to a photon-dominated region (PDR). Finally, as an example of the expected capability, the hydrochemical evolution of a PDR is presented based on the PDR benchmark.

79 ASTRONOMY AND ASTROPHYSICS↗

PHOTOSPHERIC EMISSION FROM COLLAPSAR JETS IN 3D RELATIVISTIC HYDRODYNAMICS

We explore the photospheric emission from a relativistic jet breaking out from a massive stellar envelope based on relativistic hydrodynamical simulations and post-process radiation transfer calculations in three dimensions. To investigate the impact of three-dimensional (3D) dynamics on the emission, two models of injection conditions are considered for the jet at the center of the progenitor star: one with periodic precession and another without precession. We show that structures developed within the jet due to the interaction with the stellar envelope, as well as due to the precession, have a significant imprint on the resulting emission. Particularly, we find that the signature of precession activity by the central engine is not smeared out and can be directly observed in the light curve as a periodic signal. We also show that non-thermal features, which can account for observations of gamma-ray bursts, are produced in the resulting spectra even though only thermal photons are injected initially and the effect of non-thermal particles is not considered.

79 ASTRONOMY AND ASTROPHYSICS↗

Microscopic predictions for the production of neutron-rich nuclei in the reaction Yb 176 + Yb 176

Background: Production of neutron-rich nuclei is of vital importance to both understanding nuclear structure far from stability and to informing astrophysical models of the rapid neutron capture process (r-process). Multinucleon transfer (MNT) in heavy-ion collisions offers a possibility to produce neutron-rich nuclei far from stability. Purpose: The 176 Yb + 176 Yb reaction has been suggested as a potential candidate to explore the neutron-rich region surrounding the principal fragments. The current study has been conducted with the goal of providing guidance for future experiments wishing to study this (or similar) system. Methods: Time-dependent Hartree-Fock (TDHF) and its time-dependent random-phase approximation (TDRPA) extension are used to examine both scattering and MNT characteristics in 176 Yb + 176 Yb. TDRPA calculations are performed to compute fluctuations and correlations of the neutron and proton numbers, allowing for estimates of primary fragment production probabilities. Results: Both scattering results from TDHF and transfer results from the TDRPA are presented for different energies, orvientations, and impact parameters. In addition to fragment composition, scattering angles and total kinetic energies, as well as correlations between these observables are presented. Conclusions: 176 Yb + 176 Yb appears to be an interesting probe for the midmass neutron-rich region of the chart of nuclides. Lastly, the predictions of both TDHF and TDRPA are speculative, and will benefit from future experimental results to test the validity of this approach to studying MNT in heavy, symmetric collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Kinetic Simulations of the Interruption of Large-Amplitude Shear-Alfvén Waves in a High- β Plasma

Using two-dimensional hybrid-kinetic simulations, we explore the nonlinear “interruption” of standing and traveling shear-Alfvén waves in collisionless plasmas. Interruption involves a self-generated pressure anisotropy removing the restoring force of a linearly polarized Alfvénic perturbation, and occurs for wave amplitudes δB ⊥ /B 0 ≳β –1/2 (where β is the ratio of thermal to magnetic pressure). We use highly elongated domains to obtain maximal scale separation between the wave and the ion gyroscale. For standing waves above the amplitude limit, we find that the large-scale magnetic field of the wave decays rapidly. The dynamics are strongly affected by the excitation of oblique firehose modes, which transition into long-lived parallel fluctuations at the ion gyroscale and cause significant particle scattering. Traveling waves are damped more slowly, but are also influenced by small-scale parallel fluctuations created by the decay of firehose modes. Our results demonstrate that collisionless plasmas cannot support linearly polarized Alfvén waves above δB ⊥ /B 0 ~β –1/2 . Here, they also provide a vivid illustration of two key aspects of low-collisionality plasma dynamics: (i) the importance of velocity-space instabilities in regulating plasma dynamics at high β, and (ii) how nonlinear collisionless processes can transfer mechanical energy directly from the largest scales into thermal energy and microscale fluctuations, without the need for a scale-by-scale turbulent cascade.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The Role of Mobility Data Hubs in an Integrated Decarbonized Transportation Future

The landscape for connected mobility ecosystems is evolving rapidly as information and communication technologies lower the cost and complexity of connecting people to places, integrating transportation modes and collecting data regarding such movements. These developments have been key to unlocking new business opportunities, particularly through mobility services. While the mechanisms for data collection, processing, and transfer have made significant advances in the past decade, the broader landscape of mobility data architectures and data users remains largely unresolved. It is unclear as to whether the result will converge towards a framework that resembles a coherent quilt or a disjointed patchwork of competing visions. Initial approaches to mobility data collection and provisioning have been largely siloed - by mode or software - or held for exclusive use, however several key players are quickly realizing the need and opportunities enabled through integrated mobility data eco-systems, or mobility data hubs as referred to in this paper. As the business case for hosting mobility data hubs evolves, there is great uncertainty regarding their impact to either advance or exacerbate sustainable mobility (e.g., seamless connectivity across modes, decreased energy consumption and greenhouse gas emissions, etc.). Groups such as the United Nations and World Bank have identified data platforms as a key enabler of realizing environmental and social benefits. If designed with decarbonization in mind, we hypothesize that enhanced observability provided by these ever-expanding mobility data hubs can facilitate energy and emissions reductions that are otherwise limited by transactional barriers and knowledge asymmetry that is inherent to a more siloed approach. In this sense, integration of mobility data can help to create a competitive playing field where value is not determined by exclusivity of data, but rather the quality and uniqueness of a given service. The goals of this paper are to 1) identify key players and data architectures that are emerging in a service-based mobility market, 2) explore several use cases where mobility data hubs have enabled greater sustainability outcomes, and 3) discuss key issues that will need to be resolved to fully leverage emerging mobility data hubs towards a sustainable transportation future.

ADVANCED PROPULSION SYSTEMS,MATHEMATICS AND COMPUT↗

Asymmetric photoenzymatic incorporation of fluorinated motifs into olefins

Enzymes capable of assimilating fluorinated feedstocks are scarce. This situation poses a challenge for the biosynthesis of fluorinated compounds used in pharmaceuticals, agrochemicals, and materials. We developed a photoenzymatic hydrofluoroalkylation that integrates fluorinated motifs into olefins. The photoinduced promiscuity of flavin-dependent ene-reductases enables the generation of carbon-centered radicals from iodinated fluoroalkanes, which are directed by the photoenzyme to engage enantioselectively with olefins. This approach facilitates stereocontrol through interaction between a singular fluorinated unit and the enzyme, securing high enantioselectivity at β, γ, or δ positions of fluorinated groups through enzymatic hydrogen atom transfer—a process that is notably challenging with conventional chemocatalysis. Furthermore, this work advances enzymatic strategies for integrating fluorinated chemical feedstocks and opens avenues for asymmetric synthesis of fluorinated compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Monitoring Sulfuric Acid and Temperature Using Raman Spectroscopy and Multivariate Chemometrics

Multivariate regression models were optimized for the quantification of sulfuric acid (H 2 SO 4 ) [0–8 M] and temperature (20 °C–80 °C) in the presence of ammonium sulfate ((NH 4 ) 2 SO 4 [0–0.6 M]) using Raman spectroscopy. Optical vibrational spectroscopy is a useful nondestructive technique for the in situ analysis of complex chemical systems notoriously difficult to monitor in situ and in real-time. Multivariate analysis, a chemometrics method, can be paired with these nondestructive optical methods for determining analyte concentration and speciation in complex solutions, such as dissociated species in polyprotic acids, e.g., H 2 SO 4 . The effect of temperature is often overlooked although it can have a major influence on speciation and the corresponding Raman spectra. Here, in this study, partial least squares regression models were optimized for the quantification of H 2 SO 4 and its two deprotonated forms as a function of temperature. Measuring bisulfate as a function of temperature is particularly challenging owing to changes in the second dissociation constant. A designed training set effectively minimized the sample set size and trained a robust predictive model with percent root mean square error of <3% for H 2 SO 4 . The practical strategy employed here was demonstrated to be effective for building chemometric models that directly account for dynamic temperatures with static samples and is shown to be amenable to flow cell analysis applications with a simple calibration transfer for process monitoring applications.

D-optimal design↗

An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models

Abstract Background Sequence alignment lies at the heart of genome sequence annotation. While the BLAST suite of alignment tools has long held an important role in alignment-based sequence database search, greater sensitivity is achieved through the use of profile hidden Markov models (pHMMs). Here, we describe an FPGA hardware accelerator, called HAVAC, that targets a key bottleneck step (SSV) in the analysis pipeline of the popular pHMM alignment tool, HMMER. Results The HAVAC kernel calculates the SSV matrix at 1739 GCUPS on a $$\sim$$ ∼ $3000 Xilinx Alveo U50 FPGA accelerator card, $$\sim$$ ∼ 227× faster than the optimized SSV implementation in nhmmer . Accounting for PCI-e data transfer data processing, HAVAC is 65× faster than nhmmer’s SSV with one thread and 35× faster than nhmmer with four threads, and uses $$\sim$$ ∼ 31% the energy of a traditional high end Intel CPU. Conclusions HAVAC demonstrates the potential offered by FPGA hardware accelerators to produce dramatic speed gains in sequence annotation and related bioinformatics applications. Because these computations are performed on a co-processor, the host CPU remains free to simultaneously compute other aspects of the analysis pipeline.

59 BASIC BIOLOGICAL SCIENCES↗

Prospects and applications of plasmon-exciton interactions in the near-field regime

Plasmonics is a rapidly developing field at the boundary of fundamental sciences and device engineering, which exploits the ability of metal nanostructures to concentrate electromagnetic radiation. The principal challenge lies in achieving an efficient conversion of the plasmon-concentrated field into some form of useful energy. To date, a substantial progress has been made within the scientific community in identifying the major pathways of the plasmon energy conversion. Strategies based on the hot electron injection and the near-field energy transfer have already shown promise in a number of proof-of-principle plasmonic architectures. Nevertheless, there are several fundamental questions that need to be addressed in the future to facilitate the transition of plasmonics to a variety of applications in both light amplification and optical detection. Of particular interest is a plasmon-induced resonance energy transfer (PIRET) process that couples the plasmon evanescent field to a semiconductor absorber via dipole-dipole interaction. This relatively unexplored mechanism has emerged as a promising light conversion strategy in the areas of photovoltaics and photocatalysis and represents the main focus of the present minireview. Along these lines, we highlight the key advances in this area and review some of the challenges associated with applications of the PIRET mechanism in nanostructured systems.

36 MATERIALS SCIENCE↗

CHARACTERIZATION OF Pro-Beam LOW VOLTAGE ELECTRON BEAM WELDING MACHINE

The purpose of this paper is to present and discuss data related to the performance of a newly acquired low voltage electron beam welding machine. The machine was made by Pro-Beam AG &Co. KGaA of Germany. This machine was recently installed at LANL in building SM -39; a companion machine was installed in the production facility. The PB machine is substantially different than the EBW machines typically used at LANL and therefore, it is important to understand its characteristics as well as possible. Our basic purpose in this paper is to present basic machine performance data and to compare those with similar results from the existing EBW machines. It is hoped that this data will provide a historical record of this machine’s characteristics as well as possibly being helpful for transferring welding processes from the old EBW machines to the PB machine or comparable machines that may be purchased in the future.

Electron Beam Welding, Electron Beam Measurement↗

Wafer-scale remote epitaxy of III-V semiconductors and applications

In conventional epitaxy of single-crystalline semiconductor materials, it is challenging to separate the grown layer with the substrate due to the strong bonding at the interface. Remote epitaxy is a recently discovered method to grow single-crystalline thin films on graphene, wherein the grown film can be exfoliated at the graphene interface to form freestanding membranes. Here, we present our recent development on remote epitaxy of III-V semiconductors. We show that directly growing 2D materials on III-V substrates as a remote epitaxy template is an ideal pathway that can eliminate transfer process-related defects and can realize wafer-scale process of remote epitaxy and substrate reuse. We present the strategies to grow 2D materials on the surface of III-V materials, which is much more challenging than thermally robust substrates such as SiO2/Si or sapphire. The nucleation of III-V on 2D material-coated III-V platforms via remote interaction is investigated both experimentally and theoretically. Lastly, we show advanced remote epitaxial platforms and optoelectronic applications enabled by remote epitaxy, and the capability to recycle the III-V substrates for repeated remote epitaxy and production of freestanding III-V thin films.

Kim, Hyunseok↗