Scalable AI-assisted workflow management for detector design optimization using distributed computing
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97 MATHEMATICS AND COMPUTING↗
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Scalable high-rate, high-dimensional time-bin encoding quantum key distribution
We propose and experimentally demonstrate a new scheme for measuring high-dimensional phase states using a two-photon interference technique, which we refer to as quantum-controlled measurement. Using this scheme, we implement a d -dimensional time-phase quantum key distribution (QKD) system and achieve secret key rates of 5.26 and 8.65 Mbps using d = 2 and d = 8 quantum states, respectively, for a 4 dB channel loss, illustrating that high-dimensional time-phase QKD protocols are advantageous for low-loss quantum channels. Here, this work paves the way for practical high-dimensional QKD protocols for metropolitan-scale systems. Furthermore, our results apply equally well for other high-dimensional protocols, such as those using the spatial degree-of-freedom with orbital angular momentum states being one example.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding
Abstract Motivation The vast expansion of sequence data generated from single organisms and microbiomes has precipitated the need for faster and more sensitive methods to assess evolutionary and functional relationships between proteins. Representing proteins as sets of short peptide sequences (kmers) has been used for rapid, accurate classification of proteins into functional categories; however, this approach employs an exact-match methodology and thus may be limited in terms of sensitivity and coverage. We have previously used similarity groupings, based on the chemical properties of amino acids, to form reduced character sets and recode proteins. This amino acid recoding (AAR) approach simplifies the construction of protein representations in the form of kmer vectors, which can link sequences with distant sequence similarity and provide accurate classification of problematic protein families. Results Here, we describe Snekmer, a software tool for recoding proteins into AAR kmer vectors and performing either (i) construction of supervised classification models trained on input protein families or (ii) clustering for de novo determination of protein families. We provide examples of the operation of the tool against a set of nitrogen cycling families originally collected using both standard hidden Markov models and a larger set of proteins from Uniprot and demonstrate that our method accurately differentiates these sequences in both operation modes. Availability and implementation Snekmer is written in Python using Snakemake. Code and data used in this article, along with tutorial notebooks, are available at http://github.com/PNNL-CompBio/Snekmer under an open-source BSD-3 license. Supplementary information Supplementary data are available at Bioinformatics Advances online.
59 BASIC BIOLOGICAL SCIENCES↗
GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes
Not Available
59 BASIC BIOLOGICAL SCIENCES↗
CRAGE-mediated insertion of fluorescent chromosomal markers for accurate and scalable measurement of co-culture dynamics in Escherichia coli
Monitoring population dynamics in co-culture is necessary in engineering microbial consortia involved in distributed metabolic processes or biosensing applications. However, it remains difficult to measure strain-specific growth dynamics in high-throughput formats. This is especially vexing in plate-based functional screens leveraging whole-cell biosensors to detect specific metabolic signals. Here, we develop an experimental high-throughput co-culture system to measure and model the relationship between fluorescence and cell abundance, combining chassis-independent recombinase-assisted genome engineering (CRAGE) and whole-cell biosensing with a PemrR-green fluorescent protein (GFP) monoaromatic reporter used in plate-based functional screening. CRAGE was used to construct Escherichia coli EPI300 strains constitutively expressing red fluorescent protein (RFP) and the relationship between RFP expression and optical density (OD600) was determined throughout the EPI300 growth cycle. A linear equation describing the increase of normalized RFP fluorescence during deceleration phase was derived and used to predict biosensor strain dynamics in co-culture. Measured and predicted values were compared using flow cytometric detection methods. Induction of the biosensor lead to increased GFP fluorescence normalized to biosensor cell abundance, as expected, but a significant decrease in relative abundance of the biosensor strain in co-culture and a decrease in bulk GFP fluorescence. Taken together, these results highlight sensitivity of population dynamics to variations in metabolic activity in co-culture and the potential effect of these dynamics on the performance of functional screens in plate-based formats. The engineered strains and model used to evaluate these dynamics provide a framework for optimizing growth of synthetic co-cultures used in screening, testing and pathway engineering applications.
59 BASIC BIOLOGICAL SCIENCES↗
Scalable Parallel Measurement of Individual Nitrogen-Vacancy Centers
The nitrogen-vacancy (NV) center in diamond is a solid-state spin defect that has been widely adopted for quantum sensing and quantum information processing applications. Typically, experiments are performed either with a single isolated NV center or with an unresolved ensemble of many NV centers, resulting in a trade-off between measurement speed and spatial resolution or control over individual defects. In this work, we introduce an experimental platform that bypasses this trade-off by addressing multiple optically resolved NV centers in parallel. We perform charge- and spin-state manipulations selectively on multiple NV centers from within a larger set, and we manipulate and measure the electronic spin states of over 100 NV centers in parallel. We show that the high signal-to-noise ratio of the measurements enables the detection of shot-to-shot pairwise correlations between the spin states of 108 NV centers, corresponding to the simultaneous measurement of 5778 unique correlation coefficients. We discuss how our platform can be scaled to parallel experiments with thousands of individually resolved NV centers. These results enable parallelized high-throughput sensing experiments that retain the spatial resolution of single defects and will, thereby, help to unlock advances in applications such as single-molecule NMR and characterization of integrated circuits. In addition, our approach to multiplexing provides a natural platform for the application of recently developed correlated sensing techniques.
NV centers↗
Dispersive optical systems for scalable Raman driving of hyperfine qubits
Hyperfine atomic states are among the most promising candidates for qubit encoding in quantum information processing. In atomic systems, hyperfine transitions are typically driven through a two-photon Raman process by a laser field which is amplitude modulated at the hyperfine qubit frequency. Here we introduce a method for generating amplitude modulation by phase modulating a laser and reflecting it from a highly dispersive optical element known as a chirped Bragg grating. This approach is passively stable, offers high efficiency, and is compatible with high-power laser sources, enabling large Rabi frequencies and improved quantum coherence. We benchmark this approach by globally driving an array of approximately 300 neutral 87 Rb atomic qubits trapped in optical tweezers and obtain Rabi frequencies of 2 MHz with photon-scattering error rates of less than 2×10 -4 per π pulse. This robust approach can be directly integrated with local addressing optics in both neutral atom and trapped ion systems to facilitate high-fidelity single-qubit operations for quantum information processing.
74 ATOMIC AND MOLECULAR PHYSICS↗
Electron-phonon thermalization in a scalable method for real-time quantum dynamics
Here, we present a quantum simulation method that follows the dynamics of out-of-equilibrium many-body systems of electrons and oscillators in real time. Its cost is linear in the number of oscillators and it can probe time scales from attoseconds to hundreds of picoseconds. Contrary to Ehrenfest dynamics, it can thermalize starting from a variety of initial conditions, including electronic population inversion. While an electronic temperature can be defined in terms of a nonequilibrium entropy, a Fermi-Dirac distribution in general emerges only after thermalization. These results can be used to construct a kinetic model of electron-phonon equilibration based on the explicit quantum dynamics.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Scalable fermionic error correction in Majorana surface codes
We study the error correcting properties of Majorana surface codes (MSCs), topological quantum codes constructed out of interacting Majorana fermions, which can be used to store quantum information and perform quantum computation. Furthermore, these quantum memories suffer from purely “fermionic” errors, such as quasiparticle poisoning (QP), that have no analog in conventional platforms with bosonic qubits. In physical realizations where QP dominates, we show that errors can be corrected provided that the poisoning rate is below a threshold of ~11%. When QP is highly suppressed and fermionic bilinear (“bosonic”) errors become dominant, we find an error threshold of ~16%, which is much higher than the threshold for spin-based topological memories like the surface code or the color code. In addition, we derive lattice gauge theories to account for measurement errors. These results, together with the inherent error suppression provided by the superconducting gap in physical realizations of the MSCs, makes this a strong candidate for a robust topological quantum memory.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Scalable deep convolutional neural networks for sparse, locally dense liquid argon time projection chamber data
Not Available
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Scalable qubit representations of neutrino mixing matrices
Oscillating neutrino beams exhibit quantum coherence over distances of thousands of kilometers. Their unambiguously quantum nature suggests an appealing test system for direct quantum simulation. Such techniques may enable presently analytically intractable calculations involving multi-neutrino entanglements, such as collective neutrino oscillations in supernovae, but only once oscillation phenomenology is properly re-expressed in the language of quantum circuits. Here we resolve outstanding conceptual issues regarding encoding of arbitrarily mixed neutrino flavor states in the Hilbert space of an n-qubit quantum computer. We introduce algorithms to encode mixing and oscillation of any number of flavor-mixed neutrinos, both with and without CP-violation, with an efficient number of prescriptive input parameters in terms of sub-rotations of the PMNS matrix in standard form. As a result, examples encoded for an IBM-Q quantum computer are shown to converge to analytic predictions both with and without CP-violation.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Scalable spectral solver in Galilean coordinates for eliminating the numerical Cherenkov instability in particle-in-cell simulations of streaming plasmas
Not Available
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach and paper, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. Finally, these two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.
36 MATERIALS SCIENCE↗
Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics
We introduce a scheme for molecular simulations, the deep potential molecular dynamics (DPMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data. The neural network model preserves all the natural symmetries in the problem. It is first-principles based in the sense that there are no ad hoc components aside from the network model. We show that the proposed scheme provides an efficient and accurate protocol in a variety of systems, including bulk materials and molecules. In all these cases, DPMD gives results that are essentially indistinguishable from the original data, at a cost that scales linearly with system size.
74 ATOMIC AND MOLECULAR PHYSICS↗
Quantum Solver of Contracted Eigenvalue Equations for Scalable Molecular Simulations on Quantum Computing Devices
The accurate computation of ground and excited states of many-fermion quantum systems is one of the most consequential, contemporary challenges in the physical and computational sciences whose solution stands to benefit significantly from the advent of quantum computing devices. Existing methodologies using phase estimation or variational algorithms have potential drawbacks such as deep circuits requiring substantial error correction or non-trivial high-dimensional classical optimization. In this work, we introduce a quantum solver of contracted eigenvalue equations, the quantum analogue of classical methods for the energies and reduced density matrices of ground and excited states. The solver does not require deep circuits or difficult classical optimization and achieves an exponential speed-up over its classical counterpart. We demonstrate the algorithm though computations on both a quantum simulator and two IBM quantum processing units.
97 MATHEMATICS AND COMPUTING↗