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At least 145 records · Page 8

Benchmarking embedded chain breaking in quantum annealing*

Quantum annealing solves combinatorial optimization problems by finding the energetic ground states of an embedded Hamiltonian. However, quantum annealing dynamics under the embedded Hamiltonian may violate the principles of adiabatic evolution and generate excitations that correspond to errors in the computed solution. Here we empirically benchmark the probability of chain breaks and identify sweet spots for solving a suite of embedded Hamiltonians. We further correlate the physical location of chain breaks in the quantum annealing hardware with the underlying embedding technique and use these localized rates in a tailored post-processing strategies. Our results demonstrate how to use characterization of the quantum annealing hardware to tune the embedded Hamiltonian and remove computational errors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Antenna With Embedded Die in Glass Interposer for 6G Wireless Applications

This article presents the antenna-integrated glass interposer for D-band 6G wireless applications using dieembedding technology. Here, we implement the die-embedded package on glass substrates and characterize the electrical performance in the D-band. The electrical characterization employs embedded test dies with the 50-Ω ground–signal–ground (GSG) ports and coplanar waveguides. We achieve low-loss die-to-package transitions by using staggered dielectric vias, which are compared with the transitions of wire-bonding and flip-chip assembly. This article provides detailed information on the design, modeling, fabrication, and characterization of the die-to-package interconnects. This article also demonstrates the integration of microstrip patch antenna array and embedded dies in the D-band. The results show superior electrical performance provided by the die-embedded glass interposer. The die-to-package interconnect exhibits good matching (less than —10-dB S11) and low loss (0.2-dB loss) in the D-band. The integrated 1 × 8 patch antenna array shows 11.6-dB broadside gain and good matching with the embedded die. In addition, by using a temporary carrier, the antenna-integrated glass interposer also has great potential for further heterogeneous integration and thermal management.

42 ENGINEERING↗

A PCB-Embedded 1.2 kV SiC MOSFET Half-Bridge Package for a 22 kW AC–DC Converter

This article presents the design and analysis of a double-side-cooled printed circuit board (PCB) embedded silicon carbide (SiC) MOSFET half-bridge package with low loop inductances and an integrated gate driver. The 1.2 kV SiC MOSFET dies used in the half-bridge package are embedded in the PCB using AT&S's patented technique. The dies are cooled and electrically connected to traces in the PCB through copper-filled microvias. The design methodology accounts for both electrical and thermal performance, limiting the power-loop inductance to 2.3 nH and the maximum package temperature to less than the 175 °C limit. The integration of the gate drive circuitry allows for a high power density and 2.2 nH gate-loop inductances. At 0.12 K/W, the measured junction-to-case thermal resistance with double-sided cooling is 57% lower than that of a TO-247 package. Under similar operating conditions, the PCB-embedded half-bridge package also achieves a 5.6 times lower voltage overshoot and a 0.5% higher peak efficiency than a TO-247-based half-bridge. This article reports the first demonstration of PCB-embedded 1.2 kV SiC MOSFET packages in buck, boost, and ac–dc converters. Furthermore, the prototype three-phase ac–dc converter for an electric vehicle on-board charger is composed of six PCB-embedded half-bridge packages and achieves an efficiency of 98.2% and a power density of 182 W/in 3 .

42 ENGINEERING↗

Conformal conserved currents in embedding space

We study conformal conserved currents in arbitrary irreducible representations of the Lorentz group using the embedding space formalism. With the help of the operator product expansion, we first show that conservation conditions can be fully investigated by considering only two- and three-point correlation functions. We then find an explicitly conformally-covariant differential operator in embedding space that implements conservation based on the standard position space operator product expansion differential operator ∂μ, although the latter does not uplift to embedding space covariantly. The differential operator in embedding space that imposes conservation is the same differential operator $D_{ijA}$ used in the operator product expansion in embedding space. We provide several examples including conserved currents in irreducible representations that are not symmetric and traceless. With an eye on four-point conformal bootstrap equations for four conserved vector currents $\langle JJJJ\rangle$ and four energy-momentum tensors $\langle TTTT\rangle$, we mostly focus on conservation conditions for $\langle JJ\mathcal{O}\rangle$ and $\langle TT\mathcal{O}\rangle$. Finally, we reproduce and extend the consequences of conformal Ward identities at coincident points by determining three-point coefficients in terms of charges.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Fully embedded CuNWs/PDMS conductor with high oxidation resistance and high conductivity for stretchable electronics

Currently, copper nanowires (CuNWs) based conductors have been considered as a promising candidate in the area of stretchable electronics. But the fast degradation of CuNWs in ambient conditions largely limited their practical applications. Here, the author reports a highly conductive, stable, and stretchable conductor with CuNWs fully embedded in the surface layer of poly(dimethylsiloxane) (PDMS), which not only exhibit superb stability against oxidation, but also possess good conductivity. In the fully embedded conductor, PDMS protects the CuNWs from oxidation and increases the mechanical robustness of CuNWs networks at the same time. The stretchable conductor could maintain a low sheet resistance even after 1000 cycles of stretching under 30% of strain. In addition, fully embedded CuNWs/PDMS conductors have excellent oxidation stability even in high humidity and high temperature environments (85 °C, 85 % RH). Stretchable dipole antenna was fabricated using the fully embeded CuNWs/PDMS conductors, which could retain its sensitivity to specific radio frequencies even after 500 cycles of the stretching/releasing process. At the same time, a stretchable conductive heater was demonstrated, verifying the applicability of our fully embedded conductor. We believe that this work could opens new opportunities for CuNW-based conductor into broad practical applications.

Zhang, Bowen (ORCID:000000030432745X)↗

Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer

With recent advances in understanding the genomic underpinnings and oncogenic drivers of pathogenesis in different subtypes, it is increasingly clear that proper pretreatment diagnostics are essential for the choice of appropriate treatment options for non-small cell lung cancer (NSCLC). Tumor tissue preservation in optimal cutting temperature (OCT) compound is commonly used in the surgical suite. However, proteins recovered from OCT-embedded specimens pose a challenge for LC-MS/MS experiments, due to the large amounts of polymers present in OCT. Here we present a simple workflow for whole proteome analysis of OCT-embedded NSCLC tissue samples, which involves a simple trichloroacetic acid precipitation step. Comparisons of protein recovery between frozen versus OCT-embedded tissue showed excellent consistency with more than 9200 proteins identified. Using an isobaric labeling strategy, we quantified more than 5400 proteins in tumor versus normal OCT-embedded core needle biopsy samples. Gene ontology analysis indicated that a number of proliferative as well as squamous cell carcinoma (SqCC) marker proteins were overexpressed in the tumor, consistent with the patient’s pathology based diagnosis of “poorly differentiated SqCC”. Among the most downregulated proteins in the tumor sample, we noted a number of proteins with potential immunomodulatory functions. Finally, interrogation of the aberrantly expressed proteins using a candidate approach and cross-referencing with publicly available databases led to the identification of potential druggable targets in DNA replication and DNA damage repair pathways. We conclude that our approach allows LC-MS/MS proteomic analyses on OCT-embedded lung cancer specimens, opening the way to bring powerful proteomics into the clinic. .

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Two diverse models of embedding class one

Highlights: •The embedding of curved spacetime in higher-dimensional flat spacetime is discussed. •The focus is on two diverse models of embedding class one. •The first model is a complete wormhole solution including the junction conditions. •The second is a new model to explain the flat galactic rotation curves without the need for dark matter. -- Abstract: Embedding theorems have continued to be a topic of interest in the general theory of relativity since these help connect the classical theory to higher-dimensional manifolds. This paper deals with spacetimes of embedding class one, i.e., spacetimes that can be embedded in a five-dimensional flat spacetime. These ideas are applied to two diverse models, a complete solution for a charged wormhole admitting a one-parameter group of conformal motions and a new model to explain the flat rotation curves in spiral galaxies without the need for dark matter.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A new strategy on utilizing nitrogen doped TiO{sub 2} in nanostructured solar cells: Embedded multifunctional N-TiO{sub 2} scattering particles in mesoporous photoanode

Highlights: • N-doped TiO{sub 2} scattering particles were synthesized for embedding into commercial photoanode of dye sensitized solar cells. • Embedded scatterers improved optical and electrical features of the cells. • These multifunctional scatterers increased cell performance up to 17%. - Abstract: Aggregated sub-micron size nitrogen doped TiO{sub 2} (N-TiO{sub 2}) particles with superior optical and electrical features were successfully synthesized for embedding into commercial mesoporous TiO{sub 2} photoelectrode of dye sensitized solar cells (DSSCs) as the light scattering particles compared to undoped one. X-ray photoelectron spectroscopy and absorption spectra confirmed that the titanium dioxide is sufficiently doped by nitrogen in N-TiO{sub 2} sample. Employing these high-surface N-TiO{sub 2} in mesoporous photoelectrode of solar cells, the power conversion efficiency of 8% has been achieved which shows 17% improvement for the optimum embedded level of doping (30 wt%) compared to commercial photoelectrode without additive; while enhanced efficiency is only 3% embedding undoped sub-micron size TiO{sub 2} particles. These results can introduce the novel multifunctional photoelectrode for nanostructured solar cells with enhanced values of scattering efficiency and improved electrical features including trap states density reduction in comparison to commercial mesoporous photoelectrodes.

14 SOLAR ENERGY↗

Alloying and embedding of Cu-core/Ag-shell nanowires for ultrastable stretchable and transparent electrodes

In this paper, transparent electrodes with dense Cu@Ag alloy nanowires embedded in stretchable substrates are successfully fabricated by a high-intensity pulsed light (HIPL) technique within one step. The intense light energy not only induces rapid mutual dissolution between the Cu core and the Ag shell to form dense Cu@Ag alloy nanowires but also embeds the newly formed alloy nanowires into the stretchable substrates. The synergetic effects of alloy nanowires and embedded structures greatly improve the thermal stability of the transparent electrodes that keep high conductivity unchanged in both high temperature (140 °C) and high humidity (85 °C, 85% RH) for at least 500 h, which is much better than previous reports. The transparent electrodes also exhibit high electro-mechanical stability due to the strong adhesion between alloy nanowires and substrates, which remain stable after 1000 stretching-relaxation cycles at 30% strain. Stretchable and transparent heaters based on the alloyed and embedded electrodes have a wide outputting temperature range (up to 130 °C) and show excellent thermal stability as well as stretchability (up to 60% strain) due to the alloy nanowires and embedded structures. To sum up, this study proposes the synergetic effects of alloying and embedded structures to greatly improve the stability of Cu nanowirebased stretchable transparent electrodes, showing a huge application prospect in the field of stretchable and wearable electronics.

Zhang, Bowen↗

Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)

In this paper, we present peptide-pair encoding (PPE), a general-purpose probabilistic segmentation of protein sequences into commonly occurring variable-length sub-sequences. The idea of PPE segmentation is inspired by the byte-pair encoding (BPE) text compression algorithm, which has recently gained popularity in subword neural machine translation. We modify this algorithm by adding a sampling framework allowing for multiple ways of segmenting a sequence. PPE segmentation steps can be learned over a large set of protein sequences (Swiss-Prot) or even a domain-specific dataset and then applied to a set of unseen sequences. This representation can be widely used as the input to any downstream machine learning tasks in protein bioinformatics. In particular, here, we introduce this representation through protein motif discovery and protein sequence embedding. (i) DiMotif: we present DiMotif as an alignment-free discriminative motif discovery method and evaluate the method for finding protein motifs in three different settings: (1) comparison of DiMotif with two existing approaches on 20 distinct motif discovery problems which are experimentally verified, (2) classification-based approach for the motifs extracted for integrins, integrin-binding proteins, and biofilm formation, and (3) in sequence pattern searching for nuclear localization signal. The DiMotif, in general, obtained high recall scores, while having a comparable F1 score with other methods in the discovery of experimentally verified motifs. Having high recall suggests that the DiMotif can be used for short-list creation for further experimental investigations on motifs. In the classification-based evaluation, the extracted motifs could reliably detect the integrins, integrin-binding, and biofilm formation-related proteins on a reserved set of sequences with high F1 scores. (ii) ProtVecX: we extend k-mer based protein vector (ProtVec) embedding to variablelength protein embedding using PPE sub-sequences. We show that the new method of embedding can marginally outperform ProtVec in enzyme prediction as well as toxin prediction tasks. In addition, we conclude that the embeddings are beneficial in protein classification tasks when they are combined with raw amino acids k-mer features.

59 BASIC BIOLOGICAL SCIENCES↗

Accurate and systematically improvable density functional theory embedding for correlated wavefunctions

We analyze the sources of error in quantum embedding calculations in which an active subsystem is treated using wavefunction methods, and the remainder using density functional theory. We show that the embedding potential felt by the electrons in the active subsystem makes only a small contribution to the error of the method, whereas the error in the nonadditive exchange-correlation energy dominates. We test an MP2 correction for this term and demonstrate that the corrected embedding scheme accurately reproduces wavefunction calculations for a series of chemical reactions. Our projector-based embedding method uses localized occupied orbitals to partition the system; as with other local correlation methods, abrupt changes in the character of the localized orbitals along a reaction coordinate can lead to discontinuities in the embedded energy, but we show that these discontinuities are small and can be systematically reduced by increasing the size of the active region. Convergence of reaction energies with respect to the size of the active subsystem is shown to be rapid for all cases where the density functional treatment is able to capture the polarization of the environment, even in conjugated systems, and even when the partition cuts across a double bond.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Time-dependent potential-functional embedding theory

We introduce a time-dependent potential-functional embedding theory (TD-PFET), in which atoms are grouped into subsystems. In TD-PFET, subsystems can be propagated by different suitable time-dependent quantum mechanical methods and their interactions can be treated in a seamless, first-principles manner. TD-PFET is formulated based on the time-dependent quantum mechanics variational principle. The action of the total quantum system is written as a functional of the time-dependent embedding potential, i.e., a potential-functional formulation. By exploiting the Runge-Gross theorem, we prove the uniqueness of the time-dependent embedding potential under the constraint that all subsystems share a common embedding potential. We derive the integral equation that such an embedding potential needs to satisfy. As proof-of-principle, we demonstrate TD-PFET for a Na{sub 4} cluster, in which each Na atom is treated as one subsystem and propagated by time-dependent Kohn-Sham density functional theory (TDDFT) using the adiabatic local density approximation (ALDA). Our results agree well with a direct TDDFT calculation on the whole Na{sub 4} cluster using ALDA. We envision that TD-PFET will ultimately be useful for studying ultrafast quantum dynamics in condensed matter, where key regions are solved by highly accurate time-dependent quantum mechanics methods, and unimportant regions are solved by faster, less accurate methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Structural stability and O{sub 2} dissociation on nitrogen-doped graphene with transition metal atoms embedded: A first-principles study

By using first-principles calculations, we investigate the structural stability of nitrogen-doped (N-doped) graphene with graphitic-N, pyridinic-N and pyrrolic-N, and the transition metal (TM) atoms embedded into N-doped graphene. The structures and energetics of TM atoms from Sc to Ni embedded into N-doped graphene are studied. The TM atoms at N{sub 4}V {sub 2} forming a 4N-centered structure shows the strongest binding and the binding energies are more than 7 eV. Finally, we investigate the catalytic performance of N-doped graphene with and without TM embedding for O{sub 2} dissociation, which is a fundamental reaction in fuel cells. Compared to the pyridinic-N, the graphitic-N is more favorable to dissociate O{sub 2} molecules with a relatively low reaction barrier of 1.15 eV. However, the catalytic performance on pyridinic-N doped structure can be greatly improved by embedding TM atoms, and the energy barrier can be reduced to 0.61 eV with V atom embedded. Our results provide the stable structure of N-doped graphene and its potential applications in the oxygen reduction reactions.

36 MATERIALS SCIENCE↗

Cluster embedding of ionic systems: Point charges and extended ions

The embedding of cluster models of oxides with point charges and with extensions of the embedding which take into account the spatial extent of the cations is examined with an emphasis on the consequences of this embedding for the relative ionization and excitation energies that are measured in core-level spectroscopies. It is found that the dependence of the electronic structure of the oxides and the relative energies of different levels depend only weakly on the embedding and that relatively simple embeddings may be sufficient to provide an adequate model for determining core-level spectra. This is different from absolute values of the ionizations which, as expected, depend strongly on the details of the extended crystal; however, relative values of binding energies, as measured in photoemission, are of greater interest than the absolute values.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Relativistic two-component projection-based quantum embedding for open-shell systems

In this work, we present a relativistic quantum embedding formalism capable of variationally treating relativistic effects, including scalar-relativity and spin–orbit coupling. We extend density functional theory (DFT)-in-DFT projection-based quantum embedding to a relativistic two-component formalism, where the full spin magnetization vector form is retained throughout the embedding treatment. To benchmark various relativistic embedding schemes, spin–orbit splitting of the nominally t 2g valence manifold of W(CO) 6 , exchange coupling of [(H 3 N) 4 Cr(OH) 2 Cr(NH 3 ) 4 ] 4+ , and the dissociation potential curve of WF 6 are investigated. The relativistic embedding formalism introduced in this work is well suited for efficient modeling of open-shell systems containing late transition metal, lanthanide, and actinide molecular complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DFT-based QM/MM with Particle-Mesh Ewald for Direct, Long-Range Electrostatic Embedding

In this work, we present a DFT-based, QM/MM implementation with long-range electrostatic embedding achieved by direct real-space integration of the particle mesh Ewald (PME) computed electrostatic potential. The key transformation is the interpolation of the electrostatic potential from the PME grid to the DFT quadrature grid, from which integrals are easily evaluated utilizing standard DFT machinery. We provide benchmarks of the numerical accuracy with choice of grid size and real-space corrections, and demonstrate that good convergence is achieved while introducing nominal computational overhead. Furthermore, the approach requires only small modification to existing software packages, as is demonstrated with our implementation in the OpenMM and Psi 4 software. After presenting convergence benchmarks, we evaluate the importance of long-range electrostatic embedding in three solute/solvent systems modeled with QM/MM. Water and BMIM/BF 4 ionic liquid were considered as "simple" and "complex" solvents respectively, with water and p-phenylenediamine (PPD) solute molecules treated at QM level of theory. While electrostatic embedding with standard real-space truncation may introduce negligible error for simple systems such as water solute in water solvent, errors become more significant when QM/MM is applied to complex solvents such as ionic liquids. An extreme example is the electrostatic embedding energy for oxidized PPD in BMIM/BF 4 for which real-space truncation produces severe error even at 2-3 nm cutoff distances. This latter example illustrates that utilization of QM/MM to compute redox potentials within concentrated electrolytes/ionic media requires carefully chosen long-range electrostatic embedding algorithms, with our presented algorithm providing a general and robust approach.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Probabilistic variable-length segmentation of protein sequences for discriminative motif discovery (DiMotif) and sequence embedding (ProtVecX)

ABSTRACT In this paper, we present peptide-pair encoding (PPE), a general-purpose probabilistic segmentation of protein sequences into commonly occurring variable-length sub-sequences. The idea of PPE segmentation is inspired by the byte-pair encoding (BPE) text compression algorithm, which has recently gained popularity in subword neural machine translation. We modify this algorithm by adding a sampling framework allowing for multiple ways of segmenting a sequence. PPE segmentation steps can be learned over a large set of protein sequences (Swiss-Prot) or even a domain-specific dataset and then applied to a set of unseen sequences. This representation can be widely used as the input to any downstream machine learning tasks in protein bioinformatics. In particular, here, we introduce this representation through protein motif discovery and protein sequence embedding. (i) DiMotif: we present DiMotif as an alignment-free discriminative motif discovery method and evaluate the method for finding protein motifs in three different settings: (1) comparison of DiMotif with two existing approaches on 20 distinct motif discovery problems which are experimentally verified, (2) classification-based approach for the motifs extracted for integrins, integrin-binding proteins, and biofilm formation, and (3) in sequence pattern searching for nuclear localization signal. The DiMotif, in general, obtained high recall scores, while having a comparable F1 score with other methods in the discovery of experimentally verified motifs. Having high recall suggests that the DiMotif can be used for short-list creation for further experimental investigations on motifs. In the classification-based evaluation, the extracted motifs could reliably detect the integrins, integrin-binding, and biofilm formation-related proteins on a reserved set of sequences with high F1 scores. (ii) ProtVecX: we extend k-mer based protein vector (ProtVec) embedding to variable-length protein embedding using PPE sub-sequences. We show that the new method of embedding can marginally outperform ProtVec in enzyme prediction as well as toxin prediction tasks. In addition, we conclude that the embeddings are beneficial in protein classification tasks when they are combined with raw k-mer features. Availability Implementations of our method will be available under the Apache 2 licence at http://llp.berkeley.edu/dimotif and http://llp.berkeley.edu/protvecx .

Asgari, Ehsaneddin↗

Quantum annealing correction with minor embedding

Quantum annealing provides a promising route for the development of quantum optimization devices, but the usefulness of such devices will be limited in part by the range of implementable problems as dictated by hardware constraints. To overcome constraints imposed by restricted connectivity between qubits, a larger set of interactions can be approximated using minor embedding techniques whereby several physical qubits are used to represent a single logical qubit. However, minor embedding introduces new types of errors due to its approximate nature. Here we introduce and study quantum annealing correction schemes designed to improve the performance of quantum annealers in conjunction with minor embedding, thus leading to a hybrid scheme defined over an encoded graph. We argue that this scheme can be efficiently decoded using an energy minimization technique provided the density of errors does not exceed the per-site percolation threshold of the encoded graph. We test the hybrid scheme using a D-Wave Two processor on problems for which the encoded graph is a two-level grid and the Ising model is known to be NP-hard. The problems we consider are frustrated Ising model problem instances with “planted” (a priori known) solutions. Applied in conjunction with optimized energy penalties and decoding techniques, we find that this approach enables the quantum annealer to solve minor embedded instances with significantly higher success probability than it would without error correction. Our work demonstrates that quantum annealing correction can and should be used to improve the robustness of quantum annealing not only for natively embeddable problems but also when minor embedding is used to extend the connectivity of physical devices.

74 ATOMIC AND MOLECULAR PHYSICS↗