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At least 55 records · Page 3

Noise-Directed Adaptive Remapping for Integer Optimization: from qubits to (encoded) qudits

We extend Noise-Directed Adaptive Remapping (NDAR), a recently proposed heuristic meta-algorithm that leverages device noise as a computational resource, to optimization problems over discrete (integer) domains. While originally introduced for unconstrained binary optimization, the proposed generalization introduces additional gauge degrees of freedom at the logical level, such that the gauge transformation applied at each iteration is no longer unique, allowing tailoring to particular encodings or quantum hardware. We identify encoding-dependent requirements for NDAR beyond binary domains: feasibility of the noise attractor, existence of compatible gauge transformations that preserve an efficiently implementable circuit family, and a systematic way to select the transform to apply at each step. We analyze these criteria for qudit-native and for binary, one-hot, and domain-wall qubit encodings, using the Max-k-colorable subgraph problem as a running example. We demonstrate that these encodings can exhibit distinct advantages and tradeoffs when integrated within the NDAR framework, particularly in how noise-induced dynamics interact with the solution landscape and choice of encoding. Our results indicate that NDAR-guided noise considerations provide a new criterion for comparing device-level encoding choices for quantum optimization. Finally, we outline directions toward experimental realization in superconducting qudit devices and further algorithmic improvements.

Hadfield, Stuart [RIACS, Mtn. View] (ORCID:0000000↗

Glass Additive and Subtractive Manufacturing of a Fiber Optic Rotary Encoder for Downhole Pressure Sensing

This article presents a fiber optic rotary encoder-based pressure sensor for downhole applications. The rotary encoder, which is composed of an encoding pad and an all-glass optical fiber sensing head, converts the rotation angles of a pressure transducer to digital codes. The optical fiber only serves as the telemetry channel to directly transmit the data in digital format such that the environmental temperature influence and the long-time drift are minimized. The glass additive and subtractive manufacturing (ASM) techniques are used to embed the multichannel optical fibers into a bulk-fused silica glass substrate. Because the fused silica glass shares a similar material property to the optical fiber (e.g., thermal expansion coefficient), the optical fiber sensing head is well sealed and fixed even at an elevated temperature. The picosecond laser blackening technique is used to fabricate the high reflectivity contrast encoding pad with high accuracy. Here, the proposed pressure sensor was manufactured and experimentally verified to have a signal-to-noise ratio (SNR) of 23 dB and a linear pressure response with a root-mean-square error (RMSE) of 0.37. During the 400-h 250 °C long-term stability test, there was no digital code variation. In addition, a mathematical model to study the relationships between the sensor’s performances and design parameters was established. According to the model, a 12-bit encoder (0.02% pressure sensitivity) can be achieved with a radius of 20 mm.

02 PETROLEUM↗

Design and analysis of multi-hexagonal reversible encoder using photonic crystals

In this paper, a 4 × 2 reversible encoder with hexagonal lattice has been designed using two-dimensional photonic crystals with non-linear refractive index. In order to demonstrate the working of the encoder, we have used the multi-hexagonal shaped structure arranged in parallel with appropriate inclination to get the desired output. During its functionality as an encoder, more than 98% of the power is coupled at the output port to obtain logic 1 and less than 17.2% of the power is coupled for obtaining logic 0. In addition, during its functionality as a reversible encoder, the logic 1 and logic 0 correspond to 97.5% and 15.1%, respectively. The proposed encoder provides an improved contrast ratio of 12.18 dB and 11.5 dB for logical states of 01 and 10, respectively.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Reduction of nuclear encoded enzymes of mitochondrial energy metabolism in cells devoid of mitochondrial DNA

Highlights: Black-Right-Pointing-Pointer We examined OXPHOS and citrate synthase enzyme activities in HEK293 cells devoid of mtDNA. Black-Right-Pointing-Pointer Enzymes partially encoded by mtDNA show reduced activities. Black-Right-Pointing-Pointer Also the entirely nuclear encoded complex II and citrate synthase exhibit reduced activities. Black-Right-Pointing-Pointer Loss of mtDNA induces a feedback mechanism that downregulates complex II and citrate synthase. -- Abstract: Mitochondrial DNA (mtDNA) depletion syndromes are generally associated with reduced activities of oxidative phosphorylation (OXPHOS) enzymes that contain subunits encoded by mtDNA. Conversely, entirely nuclear encoded mitochondrial enzymes in these syndromes, such as the tricarboxylic acid cycle enzyme citrate synthase (CS) and OXPHOS complex II, usually exhibit normal or compensatory enhanced activities. Here we report that a human cell line devoid of mtDNA (HEK293 {rho}{sup 0} cells) has diminished activities of both complex II and CS. This finding indicates the existence of a feedback mechanism in {rho}{sup 0} cells that downregulates the expression of entirely nuclear encoded components of mitochondrial energy metabolism.

60 APPLIED LIFE SCIENCES↗

TsPAP1 encodes a novel plant prolyl aminopeptidase whose expression is induced in response to suboptimal growth conditions

Highlights: Black-Right-Pointing-Pointer A cDNA encoding a novel plant prolyl aminopeptidase, TsPAP1, was obtained from triticale. Black-Right-Pointing-Pointer The cloned TsPAP1 cDNA is 1387 bp long and encodes a protein of 390 amino acids. Black-Right-Pointing-Pointer The deduced TsPAP1 protein revealed characteristics of the monomeric bacterial PAPs. Black-Right-Pointing-Pointer The TsPAP1 mRNA level increased under drought, salinity and in the presence of metal ions. -- Abstract: A triticale cDNA encoding a prolyl aminopeptidase (PAP) was obtained by RT-PCR and has been designated as TsPAP1. The cloned cDNA is 1387 bp long and encodes a protein of 390 amino acids with a calculated molecular mass of 43.9 kDa. The deduced TsPAP1 protein exhibits a considerable sequence identity with the biochemically characterized bacterial and fungal PAP proteins of small molecular masses ({approx}35 kDa). Moreover, the presence of conserved regions that are characteristic for bacterial monomeric PAP enzymes (the GGSWG motif, the localization of the catalytic triad residues and the segment involved in substrate binding) has also been noted. Primary structure analysis and phylogenetic analysis revealed that TsPAP1 encodes a novel plant PAP protein that is distinct from the multimeric proteins that have thus far been characterized in plants and whose counterparts have been recognized only in bacteria and fungi. A significant increase in the TsPAP1 transcript level in the shoots of triticale plants was observed under drought and saline conditions as well as in the presence of cadmium and aluminium ions in the nutrient medium. This paper is the first report describing changes in the transcript levels of any plant PAP in response to suboptimal growth conditions.

60 APPLIED LIFE SCIENCES↗

Fault-tolerant resource comparison of qudit and qubit encodings for diagonal quadratic operators

Finite local Hilbert-space truncations arise naturally in quantum simulations of lattice field theories and motivate qudit encodings, but their fault-tolerant advantage over qubit encodings remains unclear. We compare the non-Clifford cost of implementing quadratic diagonal evolutions, exemplified by 𝑈 = 𝑒$^{−𝑖⁢𝑡⁢𝜙^2_𝑥}$ in a uniform field-amplitude discretization of a real scalar field, using either one logical 𝑑-level qudit or 𝑛 𝑏 = ⌈log 2⁡ 𝑑⌉ logical qubits. We analyze two standard settings: product-formula simulation and linear combination of unitaries (LCU) per block encoding, taking the resource metric to be the number of non-Clifford gates after synthesis into a discrete logical gate set. Because tight synthesis bounds for general single-qudit rotations are not known, we express the qudit constructions in terms of embedded two-level SU⁡(2) rotations and derive explicit finite-𝑑 break-even conditions for their synthesis cost; these serve as compiler targets for when qudit encodings can outperform the qubit baseline. Within the constructive models studied here, product-formula implementations would require an exponentially stronger per-primitive synthesis advantage for qudits to win asymptotically, while in the LCU setting the qubit encoding is asymptotically cheaper in 𝑑. Nevertheless, the finite-𝑑 threshold analysis identifies low-dimensional regions in which qudits can yield meaningful constant-factor savings, particularly for LCU-based implementations. As a secondary analysis of the LCU construction, we use an idealized negligible-overhead qubit-qudit code-switching model to give an absolute 𝑇-count comparison and reinterpret the savings as an allowable per-switch overhead budget.

Godwood, Samuel [Univ. of Liverpool (United Kingdo↗

Many-fermion simulation from the contracted quantum eigensolver without fermionic encoding of the wave function

Quantum computers potentially have an exponential advantage over classical computers for the quantum simulation of many-fermion quantum systems. Nonetheless, fermions are more expensive to simulate than bosons due to the fermionic encoding—a mapping by which the qubits are encoded with fermion statistics. Here we generalize the contracted quantum eigensolver (CQE) to avoid fermionic encoding of the wave function. In contrast to the variational quantum eigensolver, the CQE solves for a many-fermion stationary state by minimizing the contraction (projection) of the Schrödinger equation onto two fermions. We avoid fermionic encoding of the wave function by contracting the Schrödinger equation onto an unencoded pair of particles. Solution of the resulting contracted equation by a series of unencoded two-body exponential transformations generates an unencoded wave function from which the energy and two-fermion reduced density matrix (2-RDM) can be computed. We apply the unencoded and the encoded CQE algorithms to the hydrogen fluoride molecule, the dissociation of oxygen O 2 , and a series of hydrogen chains. Both algorithms show comparable convergence towards the exact ground-state energies and 2-RDMs, but the unencoded algorithm has computational advantages in terms of state preparation and tomography.

74 ATOMIC AND MOLECULAR PHYSICS↗

Fidelity of an encoded [7,1,3] logical zero

I calculate the fidelity of a [7,1,3] Calderbank-Shor-Steane quantum error correction code logical zero state constructed in a nonequiprobable Pauli operator error environment for two methods of encoding. The first method is to apply fault-tolerant error correction to an arbitrary state of seven qubits utilizing Shor states for syndrome measurement. The Shor states are themselves constructed in the nonequiprobable Pauli operator error environment, and their fidelity depends on the number of verifications done to ensure multiple errors will not propagate into the encoded quantum information. Surprisingly, performing these verifications may lower the fidelity of the constructed Shor states. The second encoding method is to simply implement the [7,1,3] encoding gate sequence also in the nonequiprobable Pauli operator error environment. Perfect error correction is applied after both methods to determine the correctability of the implemented errors. I find that which method attains higher fidelity depends on which of the Pauli operators errors is dominant. Nevertheless, perfect error correction applied after the encoding suppresses errors to at least first order for both methods.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

CovS inactivation reduces CovR promoter binding at diverse virulence factor encoding genes in group A Streptococcus

The control of virulence gene regulator (CovR), also called caspsule synthesis regulator (CsrR), is critical to how the major human pathogen group A Streptococcus fine-tunes virulence factor production. CovR phosphorylation (CovR~P) levels are determined by its cognate sensor kinase CovS, and functional abrogating mutations in CovS can occur in invasive GAS isolates leading to hypervirulence. Presently, the mechanism of CovR-DNA binding specificity is unclear, and the impact of CovS inactivation on global CovR binding has not been assessed. Thus, we performed CovR chromatin immunoprecipitation sequencing (ChIP-seq) analysis in the emm1 strain MGAS2221 and its CovS kinase deficient derivative strain 2221-CovS-E281A. We identified that CovR bound in the promoter regions of nearly all virulence factor encoding genes in the CovR regulon. Additionally, direct CovR binding was observed for numerous genes encoding proteins involved in amino acid metabolism, but we found limited direct CovR binding to genes encoding other transcriptional regulators. The consensus sequence AATRANAAAARVABTAAA was present in the promoters of genes directly regulated by CovR, and mutations of highly conserved positions within this motif relieved CovR repression of the hasA and MGAS2221_0187 promoters. Analysis of strain 2221-CovS-E281A revealed that binding of CovR at repressed, but not activated, promoters is highly dependent on CovR~P state. CovR repressed virulence factor encoding genes could be grouped dependent on how CovR~P dependent variation in DNA binding correlated with gene transcript levels. Taken together, the data show that CovR repression of virulence factor encoding genes is primarily direct in nature, involves binding to a newly-identified DNA binding motif, and is relieved by CovS inactivation. These data provide new mechanistic insights into one of the most important bacterial virulence regulators and allow for subsequent focused investigations into how CovR-DNA interaction at directly controlled promoters impacts GAS pathogenesis.

59 BASIC BIOLOGICAL SCIENCES↗

Encoding trade-offs and design toolkits in quantum algorithms for discrete optimization: coloring, routing, scheduling, and other problems

Challenging combinatorial optimization problems are ubiquitous in science and engineering. Several quantum methods for optimization have recently been developed, in different settings including both exact and approximate solvers. Addressing this field of research, this manuscript has three distinct purposes. First, we present an intuitive method for synthesizing and analyzing discrete (i.e., integer-based) optimization problems, wherein the problem and corresponding algorithmic primitives are expressed using a discrete quantum intermediate representation (DQIR) that is encoding-independent. This compact representation often allows for more efficient problem compilation, automated analyses of different encoding choices, easier interpretability, more complex runtime procedures, and richer programmability, as compared to previous approaches, which we demonstrate with a number of examples. Second, we perform numerical studies comparing several qubit encodings; the results exhibit a number of preliminary trends that help guide the choice of encoding for a particular set of hardware and a particular problem and algorithm. Our study includes problems related to graph coloring, the traveling salesperson problem, factory/machine scheduling, financial portfolio rebalancing, and integer linear programming. Third, we design low-depth graph-derived partial mixers (GDPMs) up to 16-level quantum variables, demonstrating that compact (binary) encodings are more amenable to QAOA than previously understood. We expect this toolkit of programming abstractions and low-level building blocks to aid in designing quantum algorithms for discrete combinatorial problems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Explicit block encodings of boundary value problems for many-body elliptic operators

Simulation of physical systems is one of the most promising use cases of future digital quantum computers. In this work we systematically analyze the quantum circuit complexities of block encoding the discretized elliptic operators that arise extensively in numerical simulations for partial differential equations, including high-dimensional instances for many-body simulations. When restricted to rectangular domains with separable boundary conditions, we provide explicit circuits to block encode the many-body Laplacian with separable periodic, Dirichlet, Neumann, and Robin boundary conditions, using standard discretization techniques from low-order finite difference methods. To obtain high-precision, we introduce a scheme based on periodic extensions to solve Dirichlet and Neumann boundary value problems using a high-order finite difference method, with only a constant increase in total circuit depth and subnormalization factor. We then present a scheme to implement block encodings of differential operators acting on more arbitrary domains, inspired by Cartesian immersed boundary methods. We then block encode the many-body convective operator, which describes interacting particles experiencing a force generated by a pair-wise potential given as an inverse power law of the interparticle distance. This work provides concrete recipes that are readily translated into quantum circuits, with depth logarithmic in the total Hilbert space dimension, that block encode operators arising broadly in applications involving the quantum simulation of quantum and classical many-body mechanics.

Kharazi, Tyler [University of California, Berkeley↗

Encoding of symbols for a computer interconnect based on frequency of symbol values

Data are serially communicated over an interconnect between an encoder and a decoder. The encoder includes a first training unit to count a frequency of symbol values in symbol blocks of a set of N number of symbol blocks in an epoch. A circular shift unit of the encoder stores a set of most-recently-used (MRU) amplitude values. An XOR unit is coupled to the first training unit and the first circular shift unit as inputs and to the interconnect as output. A transmitter is coupled to the encoder XOR unit and the interconnect and thereby contemporaneously sends symbols and trains on the symbols. In a system, a device includes a receiver and decoder that receive, from the encoder, symbols over the interconnect. The decoder includes its own training unit for decoding the transmitted symbols.

SeyedzadehDelcheh, SeyedMohammad↗

Epstein-Barr virus-encoded latent membrane protein 1 induces epithelial to mesenchymal transition by inducing V-set Ig domain containing 4 (VSIG4) expression via NF-kB in renal tubular epithelial HK-2 cells

The epithelial to mesenchymal transition (EMT), a hallmark of chronic kidney disease, is a key event in the conversion from tubular epithelial cells to myofibroblasts in renal fibrosis. Epstein-Barr virus (EBV) is a γ-herpes oncovirus associated with chronic kidney disease. However, the relationship between EBV and the EMT process in renal tubular epithelial cells is not well understood. Among EBV-latent genes, EBV-encoded latent membrane protein 1 (LMP1) induces EMT by regulating a variety of molecules in EBV-induced oncogenic transformation. In this study, we investigated EBV-encoded LMP1 and EMT process markers in human proximal tubule epithelial cell line HK-2. LMP1 overexpression induces cell morphological changes via the epithelial to mesenchymal process in HK-2 cells, and these changes accelerate cell proliferation, cell motility, and invasion. Furthermore, VSIG4 upregulation by EBV-LMP1 induced LMP1-mediated EMT, cell motility, and invasion. VSIG4 upregulation by LMP1 was regulated at the transcriptional level via the NF-kB signaling axis. These results suggest that EBV-encoded LMP1 regulates EMT through the NF-kB-VSIG4 axis in HK-2 cells, and VSIG4 is a potential target in EBV-induced chronic kidney diseases. - Highlights: • Epstein Barr virus-encoded LMP1 overexpression induces epithelial to mesenchymal transition in renal epithelial HK-2 cells. • Upregulation of VISG4 expression by EBV-LMP1 plays an important role in LMP1-induced EMT process in HK-2 cells. • VSIG4 upregulation by EBV-LMP1 is regulated at transcriptional level via LMP1-induced NF-kB activation. • The interruption of VSIG4 expression could be a potential strategy for treatment of EBV-infected renal diseases.

60 APPLIED LIFE SCIENCES↗

An encoder–decoder LSTM-based EMPC framework applied to a building HVAC system

Numerous studies have demonstrated the benefit of economic model predictive control (EMPC) applied to building heating, ventilation, and air conditioning (HVAC) systems. However, the construction and training of predictive models for building HVAC systems are widely recognized as a key technological barrier preventing large-scale adoption of EMPC for buildings. In this work, an encoder–decoder long short-term memory-based EMPC framework is developed. The key advantage of the approach is that a model may be automatically generated from a list of inputs and outputs. From the definition of inputs and outputs, the constructed model may be trained and automatically embedded into the EMPC framework for real-time estimation and control. The overall end-to-end EMPC framework from model training to on-line estimation and control are described. To this end, the encoder–decoder model provides a natural framework for state estimation (encoder), which is required to provide an initial condition for the predictive model of EMPC (decoder). Closed-loop simulations using EnergyPlus are performed to demonstrate the approach. The simulated closed-loop system consists of a building zone from a multi-zone building, which is served by an air handling unit-variable air volume HVAC system. For the HVAC example considered, the trained encoder–decoder model can predict the indoor air temperature and HVAC sensible cooling rate of a building zone over a two-day horizon with high accuracy. Overall, we find that considering a time-of-use electric rate structure, the EMPC, which manipulates the zone temperature setpoint, can reduce the HVAC power consumption cost relative to keeping the zone temperature setpoint at its maximum value (i.e., minimum energy approach).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Bacteriophage SP6 encodes a second tailspike protein that recognizes Salmonella enterica serogroups C{sub 2} and C{sub 3}

SP6 is a salmonella phage closely related to coliphage K1-5. K1-5 is notable in that it encodes two polysaccharide-degrading tailspike proteins, an endosialidase that allows it to infect E. coli K1, and a lyase that enables it to infect K5 strains. SP6 is similar to K1-5 except that it encodes a P22-like endorhamnosidase tailspike, gp46, allowing it to infect group B Salmonella. We show here that SP6 can also infect Salmonella serogroups C{sub 2} and C{sub 3} and that a mutation in a putative second tailspike, gp47, eliminates this specificity. Gene 47 was fused to the coding region of the N-terminal portion of the Pseudomonas aeruginosa R2 pyocin tail fiber and expressed in trans such that the fusion protein becomes incorporated into pyocin particles. These pyocins, termed AvR2-SP47, killed serogroups C{sub 2} and C{sub 3}Salmonella. We conclude that SP6 encodes two tail proteins providing it a broad host range among Salmonella enterica. - Highlights: • SP6 is a “dual specificity” bacteriophage that encodes two different receptor binding proteins giving it a broad host range. • These receptor binding proteins can be used to re-target the spectrum of R-type bacteriocins to Salmonella enterica. • Both SP6 and the engineered R-type bacteriocins can kill the Salmonella serovars most associated with human disease making them attractive for development as antimicrobial agents.

60 APPLIED LIFE SCIENCES↗

Numerous cultivated and uncultivated viruses encode ribosomal proteins

Viruses modulate ecosystems by directly altering host metabolisms through auxiliary metabolic genes. However, viral genomes are not known to encode the core components of translation machinery, such as ribosomal proteins (RPs). Here, using reference genomes and global-scale viral metagenomic datasets, we identify 14 different RPs across viral genomes arising from cultivated viral isolates and metagenome-assembled viruses. Viruses tend to encode dynamic RPs, easily exchangeable between ribosomes, suggesting these proteins can replace cellular versions in host ribosomes. Functional assays confirm that the two most common virus-encoded RPs, bS21 and bL12, are incorporated into 70S ribosomes when expressed in Escherichia coli. Ecological distribution of virus-encoded RPs suggests some level of ecosystem adaptations as aquatic viruses and viruses of animal-associated bacteria are enriched for different subsets of RPs. Finally, RP genes are under purifying selection and thus likely retained an important function after being horizontally transferred into virus genomes.

59 BASIC BIOLOGICAL SCIENCES↗

Orthogonal luminescence lifetime encoding by intermetallic energy transfer in heterometallic rare-earth MOFs

Lifetime-encoded materials are particularly attractive as optical tags, however examples are rare and hindered in practical application by complex interrogation methods. Here, we demonstrate a design strategy towards multiplexed, lifetime-encoded tags via engineering intermetallic energy transfer in a family of heterometallic rare-earth metal-organic frameworks (MOFs). The MOFs are derived from a combination of a high-energy donor (Eu), a low-energy acceptor (Yb) and an optically inactive ion (Gd) with the 1,2,4,5 tetrakis(4-carboxyphenyl) benzene (TCPB) organic linker. Precise manipulation of the luminescence decay dynamics over a wide microsecond regime is achieved via control over metal distribution in these systems. Demonstration of this platform’s relevance as a tag is attained via a dynamic double encoding method that uses the braille alphabet, and by incorporation into photocurable inks patterned on glass and interrogated via digital high-speed imaging. This study reveals true orthogonality in encoding using independently variable lifetime and composition, and highlights the utility of this design strategy, combining facile synthesis and interrogation with complex optical properties.

36 MATERIALS SCIENCE↗

Regioselective surface encoding of nanoparticles for programmable self-assembly

Surface encoding of colloidal nanoparticles with DNA is fundamental for fields where recognition interaction is required, particularly controllable material self-assembly. However, regioselective surface encoding of nanoparticles is still challenging because of the difficulty associated with breaking the identical chemical environment on nanoparticle surfaces. Here we demonstrate the selective blocking of nanoparticle surfaces with a diblock copolymer (polystyrene-b-polyacrylic acid). By tuning the interfacial free energies of a ternary system involving the nanoparticles, solvent and copolymer, controllable accessibilities to the nanoparticles’ surfaces are obtained. Through the modification of the polymer-free surface region with single-stranded DNA, regioselective and programmable surface encoding is realized. The resultant interparticle binding potential is selective and directional, allowing for an increased degree of complexity of potential self-assemblies. As a result, the versatility of this regioselective surface encoding strategy is demonstrated on various nanoparticles of isotropic or anisotropic shape and a total of 24 distinct complex nanoassemblies are fabricated.

77 NANOSCIENCE AND NANOTECHNOLOGY↗