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We report a three-dimensional quantum lattice algorithm (QLA) for electromagnetic wave propagation is being developed by stitching together the individual QLAs for 1D wave propagation in the three orthogonal Cartesian directions
ALS-ENABLE is an integrated NIH P30 resource at the Advanced Light Source synchrotron at Lawrence Berkeley National Laboratory in Berkeley, California, USA. The resource provides a single portal to the combined mature structural biology technologies of macromolecular crystallography, small-angle X-ray scattering and X-ray footprinting mass spectrometry, and includes beamlines 2.0.1, 3.3.1, 4.2.2, 5.0.1, 5.0.2, 5.0.3, 8.2.1, 8.2.2, 8.3.1 and 12.3.1. This paper describes the organizational structure and the technologies of ALS-ENABLE. A case study showcasing the main technologies of the resource applied to the characterization of the SpyCatcher-SpyTag protein system is presented.
During surveillance of Staphylococcus aureus in lesions from patients with atopic dermatitis (AD), we isolated Staphylococcus argenteus, a species registered in 2011 as a new member of the genus Staphylococcus and previously considered a lineage of S. aureus. Genome sequence comparisons between S. argenteus isolates and representative S. aureus clinical isolates from various origins revealed that the S. argenteus genome from AD patients closely resembles that of S. aureus causing skin infections. We previously reported that 17%–22% of S. aureus isolated from skin infections produce staphylococcal enterotoxin Y (SEY), which predominantly induces T-cell proliferation via the T-cell receptor (TCR) Vα pathway. Complete genome sequencing of S. argenteus isolates revealed a gene encoding a protein similar to superantigen SEY, designated as SargEY, on its chromosome. Population structure analysis of S. argenteus revealed that these isolates are ST2250 lineage, which was the only lineage positive for the SEY-like gene among S. argenteus. Recombinant SargEY demonstrated immunological cross-reactivity with anti-SEY serum. SargEY could induce proliferation of human CD4 + and CD8 + T cells, as well as production of TNF-α and IFN-γ. SargEY showed emetic activity in a marmoset monkey model. S arg EY and SET (a phylogenetically close but uncharacterized SE) revealed their dependency on TCR Vα in inducing human T-cell proliferation. Additionally, TCR sequencing revealed other previously undescribed Vα repertoires induced by SEH. S arg EY and SEY may play roles in exacerbating the respective toxin-producing strains in AD.
This final technical report summarizes research conducted under DOE Award DE-SC0021653 to develop unitary Quantum Lattice Algorithms for modeling electromagnetic wave propagation and scattering in complex media, including plasmas. The project developed and validated quantum-inspired formulations of Maxwell's equations that preserve unitary evolution and can be evaluated on classical high-performance computing systems while providing a foundation for future quantum-computing implementations. Major accomplishments include the development of two- and three-dimensional algorithms for electromagnetic scattering; scalable, distributed-memory implementations demonstrated on the Perlmutter supercomputer; formulations for nonlinear lossless fluid dynamics and cold, lossless, inhomogeneous magnetized plasmas; and an explicit quantum algorithm for a time-discretized Lorenz model. Simulations reproduced a range of characteristic wave phenomena, including transient effects that are not readily apparent in conventional frequency-domain studies, demonstrating the effectiveness of the proposed approach for modeling complex electromagnetic and plasma systems. The work establishes a unified theoretical and computational framework for quantum and quantum-inspired simulation and provides a foundation for future implementation on fault-tolerant quantum systems.
Background: Metastatic differentiated thyroid cancer (DTC) represents a molecularly heterogeneous group of cancers with varying radioactive iodine (RAI) and [ 18 F]-fluorodeoxyglucose (FDG) uptake patterns potentially correlated with the degree of de-differentiation through the so-called “flip-flop” phenomenon. However, it is unknown if RAI and FDG uptake patterns correlate with molecular status or metastatic site. Materials and Methods: A retrospective analysis of metastatic DTC patients (n = 46) with radioactive 131-iodine whole body scan (WBS) and FDG-PET imaging between 2008 and 2022 was performed. The inclusion criteria included accessible FDG-PET and WBS studies within 1 year of each other. Studies were interpreted by two blinded radiologists for iodine or FDG uptake in extrathyroidal sites including lungs, lymph nodes, and bone. Cases were stratified by BRAF V600E mutation status, histology, and a combination of tumor genotype and histology. The data were analyzed by McNemar’s Chi-square test. Results: Lung metastasis FDG uptake was significantly more common than iodine uptake (WBS: 52%, FDG: 84%, p = 0.04), but no significant differences were found for lymph or bone metastases. Lung metastasis FDG uptake was significantly more prevalent in the papillary pattern sub-cohort (WBS: 37%, FDG: 89%, p = 0.02) than the follicular pattern sub-cohort (WBS: 75%, FDG: 75%, p = 1.00). Similarly, BRAF V600E+ tumors with lung metastases also demonstrated a preponderance of FDG uptake (WBS: 29%, FDG: 93%, p = 0.02) than BRAF V600E- tumors (WBS: 83%, FDG: 83%, p = 1.00) with lung metastases. Papillary histology featured higher FDG uptake in lung metastasis (WBS: 39%, FDG: 89%, p = 0.03) compared with follicular histology (WBS: 69%, FDG: 77%, p = 1.00). Patients with papillary pattern disease, BRAF V600E+ mutation, or papillary histology had reduced agreement between both modalities in uptake at all metastatic sites compared with those with follicular pattern disease, BRAF V600E- mutation, or follicular histology. Low agreement in lymph node uptake was observed in all patients irrespective of molecular status or histology. Conclusions: The pattern of FDG-PET and radioiodine uptake is dependent on molecular status and metastatic site, with those with papillary histology or BRAF V600E+ mutation featuring increased FDG uptake in distant metastasis. Further study with an expanded cohort may identify which patients may benefit from specific imaging modalities to recognize and surveil metastases.
It is well known that Maxwell equations can be expressed in a unitary Schrodinger-Dirac representation for homogeneous media. However, difficulties arise when considering inhomogeneous media. A Dyson map points to a unitary field qubit basis, but the standard qubit lattice algorithm of interleaved unitary collision-stream operators must be augmented by some sparse non-unitary potential operators that recover the derivatives on the refractive indices. Here, the effect of the steepness of these derivatives on two-dimensional scattering is examined with simulations showing quite complex wavefronts emitted due to transmissions/reflections within the dielectric objects. Maxwell equations are extended to handle dissipation using Kraus operators. Then, our theoretical algorithms are extended to these open quantum systems. A quantum circuit diagram is presented as well as estimates on the required number of quantum gates for implementation on a quantum computer.
Long time quantum lattice algorithm (QLA) simulations are performed for the mul- tiple reflection-transmission of an initial electromagnetic pulse propagating normally to a boundary layer region joining two media of different refractive index. For these one dimensional (1D) sim- ulations, there is excellent agreement between x-, y- and z- representations, as well as very good agreement with nearly all the standard plane wave boundary condition results for reflection and transmission off a dielectric discontinuity. In the QLA simulation, no boundary conditions are im- posed at the continuous, but sharply increasing, dielectic boundary layers. Two dimensional (2D) QLA scattering simulations in the x-z plane are performed for an electromagnetic pulse interacting with a conical dielectric obstacle for the 8-16 qubit model.
A three-dimensional quantum lattice algorithm (QLA) for electromagnetic wave propagation is being developed by stitching together the individual QLAs for 1D wave propagation in the three orthogonal Cartesian directions.
A quantum lattice algorithm (QLA) is developed for Maxwell equations in scalar dielectric media using the Riemann-Silberstein representation on a Cartesian grid. For x-dependent and y-dependent dielectric inhomogeneities, the corresponding QLA requires a minimum of 8 qubits/spatial lattice site. This is because the corresponding Pauli spin matrices have off-diagonal components which permit the local collisional entanglement of these qubits. However, z-dependent inhomogeneities require a QLA with a minimum of 16 qubits/lattice site since the Pauli spin matrix σz is diagonal. For 2 dimensional inhomogeneities, one can readily couple the 8-8 qubit schemes for x-y variations. z-x and y-z variations can be treated by either a 16-8 qubit scheme or a 16-16 qubit representation.
There is considerable interest in the application of quantum information science to advance computations in plasma physics. A particular point of curiosity is whether it is possible to take advantage of quantum computers to speed up numerical simulations relative to conventional computers. Many of the topics in fusion plasma physics are classical in nature. In order to implement them on quantum computers it will require couching a classical problem in the language of quantum mechanics. Electromagnetic waves are routinely used in fusion experiments to heat a plasma or to generate currents in the plasma. The propagation of electromagnetic waves is described by Maxwell equations with an appropriate description of the plasma as a dielectric medium. Before advancing to the tensor dielectric of a magnetized plasma, this paper considers electromagnetic wave propagation in a one-dimensional inhomogeneous scalar dielectric. The classic theory of scattering of plane electromagnetic waves at a planar interface, separating two different dielectric media, leads to Fresnel equations for reflection and transmission coefficients. In contrast to plane waves, this paper is on the reflection and transmission of a spatially confined electromagnetic pulse. Following an analytical formulation for the scattering of a Gaussian pulse, it is deduced that the maximum transmission coefficient for a pulse is $\sqrt{n_2/n_1}$ times that for a plane wave; the incident and transmitted pulses propagating in dielectric media with refractive indices $n_1$ and $n_2$, respectively. The analytical theory is complemented by numerical simulations using a quantum lattice algorithm for Maxwell equations. The algorithm, based on the Riemann-Silberstein-Weber representation of the electromagnetic fields and expressed in term of qubits, is an interleaved sequence of entangling operators at each lattice site and unitary streaming operators which transmit information from one site to an adjacent lattice site. Besides substantiating results from the theory for Gaussian pulses, numerical simulations show their validity for non-Gaussian pulses. Apart from their time-asymptotic forms, the simulations display an interplay between the incident, reflected, and transmitted pulses in the vicinity of the transition region between two dielectric media.
It is well known that Maxwell equations can be expressed in a unitary Schrodinger-Dirac representation for homogeneous media. However, difficulties arise when considering inhomoge- neous media. A Dyson map points to a unitary field qubit basis, but the standard qubit lattice algorithm of interleaved unitary collision-stream operators must be augmented by some sparse non-unitary potential operators that recover the derivatives on the refractive indices. The effect of the steepness of these derivatives on two dimensional scattering is examined with simulations showing quite complex wavefronts emitted due to transmissions/reflections within the dielectric objects. Maxwell equations are extended to handle dissipation using Kraus operators. Then, our theoretical algorithms are extended to these open quantum systems. A quantum circuit diagram is presented as well as estimates on the required number of quantum gates for implementation on a quantum computer.