Resilient Control of Cyber-Physical System Using Nonlinear Encoding Signal Against System Integrity Attacks
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Automation & Control Systems↗
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Block encoding bosons by signal processing
Block Encoding (BE) is a crucial subroutine in many modern quantum algorithms, including those with near-optimal scaling for simulating quantum many-body systems, which often rely on Quantum Signal Processing (QSP). Currently, the primary methods for constructing BEs are the Linear Combination of Unitaries (LCU) and the sparse oracle approach. In this work, we demonstrate that QSP-based techniques, such as Quantum Singular Value Transformation (QSVT) and Quantum Eigenvalue Transformation for Unitary Matrices (QETU), can themselves be efficiently utilized for BE implementation. Specifically, we present several examples of using QSVT and QETU algorithms, along with their combinations, to block encode Hamiltonians for lattice bosons, an essential ingredient in simulations of high-energy physics. We also introduce a straightforward approach to BE based on the exact implementation of Linear Operators Via Exponentiation and LCU (LOVE-LCU). We find that, while using QSVT for BE results in the best asymptotic gate count scaling with the number of qubits per site, LOVE-LCU outperforms all other methods for operators acting on up to qubits, highlighting the importance of concrete circuit constructions over mere comparisons of asymptotic scalings. Using LOVE-LCU to implement the BE, we simulate the time evolution of single-site and two-site systems in the lattice theory using the Generalized QSP algorithm and compare the gate counts to those required for Trotter simulation.
Kane, Christopher F↗
Parameter Estimation for Decoding Sensor Signals
This paper introduces a parameter estimation approach for decoding digital sensor signals in a cyber-physical system. For unknown or not fully characterized digital sensor data, it can be difficult to decipher a desired signal from background or noise. In a cyber-physical system with networked sensors, we can leverage knowledge of the physical system to inform the decoding of the digital signals. This work in progress is a case study on deciphering commercial vehicle on-board sensor networks that communicate through the Controller Area Network (CAN). By understanding the stock vehicle sensor network, a vehicle can be extended into a scalable research platform with minimal instrumentation. Our challenge was to localize desired sensor signals encoded in network traffic that included other sensor data, control messages, as well as encoding and security overhead. Due to the vehicle’s unknown sensor network, our approach developed methods to efficiently analyze and identify key signals despite the large state-space for potential signal embeddings.
Nice, Matthew↗
A shadow detector for photosynthesis efficiency
Plants tolerate large variations in the intensity of the light environment by controlling the efficiency of solar to chemical energy conversion. To do this, plants have a mechanism to detect the intensity, duration, and change in light as they experience moving shadows, flickering light, and cloud cover. Sugars are the primary products of CO 2 fixation, a metabolic pathway that is rate limited by this solar energy conversion. We propose that sugar is a signal encoding information about the intensity, duration and change in the light environment. We previously showed that the Arabidopsis heterotrimeric G protein complex including its receptor-like Regulator of G signaling protein, AtRGS1, detects both the concentration and the exposure time of sugars [Fu, et al 2014 Cell 156: 1084–1095]. This unique property, designated dose-duration reciprocity, is a behavior that emerges from the system architecture / system motif. Here, we show that another property of the signaling system is to detect large changes in light while at the same time, filtering types of fluctuation in light that do not affect photosynthesis efficiency. When AtRGS1 is genetically ablated, photosynthesis efficiency is reduced in a changing-but not a constant-light environment. Mathematical modeling revealed that information about changes in the light environment is encoded in the amount of free AtRGS1 that becomes compartmentalized following stimulation. We propose that this property determines when to adjust photosynthetic efficiency in an environment where light intensity changes abruptly caused by moving shadows on top of a background of light changing gradually from sun rise to sun set and fluctuating light such as that caused by fluttering leaves.
59 BASIC BIOLOGICAL SCIENCES↗
Genome analysis of Daldinia eschscholtzii strains UM 1400 and UM 1020, wood-decaying fungi isolated from human hosts
Background: Daldinia eschscholtzii is a wood-inhabiting fungus that causes wood decay under certain conditions. It has a broad host range and produces a large repertoire of potentially bioactive compounds. However, there is no extensive genome analysis on this fungal species. Results: Two fungal isolates (UM 1400 and UM 1020) from human specimens were identified as Daldinia eschscholtzii by morphological features and ITS-based phylogenetic analysis. Both genomes were similar in size with 10,822 predicted genes in UM 1400 (35.8 Mb) and 11,120 predicted genes in UM 1020 (35.5 Mb). A total of 751 gene families were shared among both UM isolates, including gene families associated with fungus-host interactions. In the CAZyme comparative analysis, both genomes were found to contain arrays of CAZyme related to plant cell wall degradation. Genes encoding secreted peptidases were found in the genomes, which encode for the peptidases involved in the degradation of structural proteins in plant cell wall. In addition, arrays of secondary metabolite backbone genes were identified in both genomes, indicating of their potential to produce bioactive secondary metabolites. Both genomes also contained an abundance of gene encoding signaling components, with three proposed MAPK cascades involved in cell wall integrity, osmoregulation, and mating/filamentation. Besides genomic evidence for degrading capability, both isolates also harbored an array of genes encoding stress response proteins that are potentially significant for adaptation to living in the hostile environments. In conclusion: Our genomic studies provide further information for the biological understanding of the D. eschscholtzii and suggest that these wood-decaying fungi are also equipped for adaptation to adverse environments in the human host.
59 BASIC BIOLOGICAL SCIENCES↗
Signal Processing of Multiplexed Optical PWM Signals for Sensor Arrays in Nuclear Environments
Safe and effective generation of terrestrial nuclear power greatly benefits from the actionable data provided by the array of sensors located throughout a plant to provide a holistic online indication of reactor operation. This array includes sensors for monitoring coolant flow and pressure, temperature and heat transfer, radiation levels, structure health monitoring, and other critical parameters for reactor operation. While sensors capable of measuring these parameters have been developed, the electronics used in the pre-amplification and analog-to-digital conversion of the small signals they produce are extremely sensitive and susceptible to damage by high-temperatures and radiation environments nuclear reactors encounter while generating power. The small signals from sensors in nuclear power plants (NPPs) are transmitted over long cable runs which introduce dispersion artifacts into the signals of interest as well as electromagnetic interference (EMI) from lighting fixtures, pumps, mains electricity, and other equipment. To overcome these challenges, a front-end digitization (FREND) platform has been developed to use radiation-tolerant electronics to multiplex, amplify, and optically encode signals from an array of sensors for transmission over an optical fiber to mitigate dispersion and EMI artifacts from long runs of electrical cabling. To recover the optically transmitted data, a signal processing scheme based on 1-dimensional template matching to an indexing channel is described herein and demonstrated to have an effective bit-depth of 9.2 bits (1%). This scheme has been validated in proof-of-concept, non-nuclear testing and preliminary experimental results show good agreement between the measured optical output and and sensor input signals. The FREND system represents a low-loss data link between sensors in nuclear environments and data acquisition hardware which is aimed at improving the signal-to-noise ratio of the data acquired from these sensors to provide better information to operators and researchers.
Sweeney, Dan↗
Excited-state vibronic wave-packet dynamics in H 2 probed by XUV transient four-wave mixing
The complex behavior of a molecular wave packet initiated by an extreme ultraviolet (XUV) pulse is investigated with noncollinear wave mixing spectroscopy. A broadband XUV pulse spanning 12-16 eV launches a wave packet in H 2 comprising a coherent superposition of multiple electronic and vibrational levels. The molecular wave packet evolves freely until a delayed few-cycle optical laser pulse arrives to induce nonlinear signals in the XUV via four-wave mixing (FWM). The angularly resolved FWM signals encode rich energy exchange processes between the optical laser field and the XUV-excited molecule. The noncollinear geometry enables spatial separation of ladder and V- or Λ-type transitions induced by the optical field. Ladder transitions, in which the energy exchange with the optical field is around 3 eV, appear off axis from the incident XUV beam. Each vibrationally revolved FWM line probes a different part of the wave packet in energy, serving as a promising tool for energetic tomography of molecular wave packets. V- or Λ-type transitions, in which the energy exchange is well under 1 eV, result in on-axis nonlinear signals. The first-order versus third-order interference of the on-axis signal serves as a mapping tool of the energy flow pathways. Intra- and interelectronic potential energy curve transitions are decisively identified. The current study opens possibilities for accessing complete dynamic information in XUV-excited complex systems.
74 ATOMIC AND MOLECULAR PHYSICS↗
Precision epoch of reionization studies with next-generation CMB experiments
Future arcminute resolution polarization data from ground-based Cosmic Microwave Background (CMB) observations can be used to estimate the contribution to the temperature power spectrum from the primary anisotropies and to uncover the signature of reionization near ℓ=1500 in the small angular-scale temperature measurements. Our projections are based on combining expected small-scale E-mode polarization measurements from Advanced ACTPol in the range 300<ℓ<3000 with simulated temperature data from the full Planck mission in the low and intermediate ℓ region, 2<ℓ<2000. We show that the six basic cosmological parameters determined from this combination of data will predict the underlying primordial temperature spectrum at high multipoles to better than 1% accuracy. Assuming an efficient cleaning from multi-frequency channels of most foregrounds in the temperature data, we investigate the sensitivity to the only residual secondary component, the kinematic Sunyaev-Zel'dovich (kSZ) term. The CMB polarization is used to break degeneracies between primordial and secondary terms present in temperature and, in effect, to remove from the temperature data all but the residual kSZ term. We estimate a 15σ detection of the diffuse homogeneous kSZ signal from expected AdvACT temperature data at ℓ>1500, leading to a measurement of the amplitude of matter density fluctuations, σ{sub 8}, at 1% precision. Alternatively, by exploring the reionization signal encoded in the patchy kSZ measurements, we bound the time and duration of the reionization with σ(z{sub re})=1.1 and σ(Δz{sub re})=0.2. We find that these constraints degrade rapidly with large beam sizes, which highlights the importance of arcminute-scale resolution for future CMB surveys.
79 ASTRONOMY AND ASTROPHYSICS↗
Convolution-based frequency domain multiplexing of SiPM readouts using the $\mathrm{DRS4}$ digitizer
Here we present 4:1 multiplexing of organic scintillators, each coupled to a silicon photomultiplier (SiPM), to reduce the need for a large number of digitizer input channels to readout highly pixelated radiation detection systems. Frequency domain multiplexing (FDM) encodes a detector pulse by assigning it a unique frequency via convolution before combining the encoded signal into a single channel. The combined signal is then read through a digitizer input channel. We have designed an FDM system to multiplex four SiPMs using DRS4 digitizer evaluation board from Paul Scherrer Institute (PSI). We demonstrate 4:1 multiplexing of the SiPM fast output signals and pulse recovery from the digitized multiplexed signal using deconvolution. The noise in the recovered pulse introduces a bias and uncertainty in the estimate of energy and timing that changes with pulse height. The relative uncertainty in the estimated energy from the recovered pulse decreases with pulse height with a maximum uncertainty of 3.1% for the low energy pulses (corresponding to 100 keV); the uncertainty in the estimated time pick-off also decreases with pulse height with a maximum uncertainty of 110 ps for the low energy pulses.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Deriving Material Properties from Feedback Error Signals in Scanning Tunneling Microscopy
Imperfections in measurements, e.g., deviations and broadening, are not devoid of information; rather, they can reveal valuable physical properties and processes. Scanning tunneling microscopy leverages a negative feedback loop to regulate the tunneling current. Practically, current fluctuates around its set point, and such deviations are considered insignificant and ignored. Here, in this study, we investigate the information embedded in these deviations. In the constant-current mode with an active feedback loop, we observe an unexpected persistent DC current offset from its set point when the tunneling junction is periodically perturbed. We demonstrate both experimentally and theoretically that such error signals encode local tunneling barrier heights and the square of local differential conductance as a consequence of the interplay between rectification and active feedback compensation. We provide evidence on the generalizability of this phenomenology to other negative feedback systems. This new approach has the potential to broadly impact physical sciences by allowing rapid measurements without lock-in amplifiers.
36 MATERIALS SCIENCE↗
Ligand-induced transmembrane conformational coupling in monomeric $\mathrm{EGFR}$
Single pass cell surface receptors regulate cellular processes by transmitting ligand-encoded signals across the plasma membrane via changes to their extracellular and intracellular conformations. This transmembrane signaling is generally initiated by ligand binding to the receptors in their monomeric form. While subsequent receptor-receptor interactions are established as key aspects of transmembrane signaling, the contribution of monomeric receptors has been challenging to isolate due to the complexity and ligand-dependence of these interactions. By combining membrane nanodiscs produced with cell-free expression, single-molecule Förster Resonance Energy Transfer measurements, and molecular dynamics simulations, we report that ligand binding induces intracellular conformational changes within monomeric, full-length epidermal growth factor receptor (EGFR). Our observations establish the existence of extracellular/intracellular conformational coupling within a single receptor molecule. We implicate a series of electrostatic interactions in the conformational coupling and find the coupling is inhibited by targeted therapeutics and mutations that also inhibit phosphorylation in cells. Collectively, these results introduce a facile mechanism to link the extracellular and intracellular regions through the single transmembrane helix of monomeric EGFR, and raise the possibility that intramolecular transmembrane conformational changes upon ligand binding are common to single-pass membrane proteins.
59 BASIC BIOLOGICAL SCIENCES↗
Multi-resolution enhancement for full-spectrum neural representations
Scientific data acquisition continues to outpace storage and analysis capabilities, making voxel-basedrepresentations increasingly intractable. Implicit neural representations (INRs) offer a promising solutionby encoding signals through coordinate-based neural networks, serving as surrogates of data, withcomputational and storage requirements scaling with network complexity rather than data dimensionality.However, smaller INRs struggle to faithfully represent multiscale structures, high-frequency informationand fine textures that constitute a large proportion of scientific measurements. We propose WIEN-INR, atheoretically guided hierarchical INR framework that distributes modelling across resolution scales andenables improved representation capacity through a novel enhancement network to recover subtle details.This multiscale architecture allows smaller networks to retain the full spatial-frequency content of thesignal as well as preserve training efficiency and lower storage cost. Evaluated on distinct raw experimentalmeasurements across scales and complexities, WIEN-INR represents a practical step towards a broaderadoption of neural representations in scientific workflows, delivering compact, robust and high-fidelityrepresentations.
Ni, Yuan [SLAC National Accelerator Laboratory (SL↗
Shubnikov–de Haas oscillations of biaxial-strain-tuned superconductors in pulsed magnetic field up to 60 T
Two-dimensional (2D) materials have gained increasing prominence not only in fundamental research but also in daily applications. However, to fully harness their potential, it is crucial to optimize their properties with an external parameter and track the electronic structure simultaneously. Magnetotransport over a wide magnetic field range is a powerful method to probe the electronic structure and, for metallic 2D materials, quantum oscillations superimposed on the transport signals encode Fermi surface parameters. In this manuscript, we utilize biaxial strain as an external tuning parameter and investigate the effects of strain on the electronic properties of two quasi-2D superconductors, MoTe 2 and RbV 3 Sb 5 , by measuring their magnetoresistance in pulsed magnetic fields up to 60 T. With a careful selection of insulating substrates, we demonstrate the possibility of both the compressive and tensile biaxial strains imposed on MoTe 2 and RbV 3 Sb 5 , respectively. For both systems, the applied strain has led to superconducting critical temperature enhancement compared to their free-standing counterparts, proving the effectiveness of this biaxial strain method at cryogenic temperatures. Clear quantum oscillations in the magnetoresistance—the Shubnikov–de Haas (SdH) effect—are obtained in both samples. In strained MoTe 2 , the magnetoresistance exhibits a nearly quadratic dependence on the magnetic field and remains non-saturating even at the highest field, whereas in strained RbV 3 Sb 5 , two SdH frequencies showed a substantial enhancement in effective mass values, hinting at a possible enhancement of charge fluctuations. Our results demonstrate that combining biaxial strain and pulsed magnetic field paves the way for studying 2D materials under unprecedented conditions.
2D materials↗
The CMS Phase-2 Fast Beam Condition Monitor prototype test with beam
The Fast Beam Condition Monitor (FBCM) is a standalone luminometer for the High Luminosity LHC (HL-LHC) program of the CMS Experiment at CERN. The detector is under development and features a new, radiation-hard, front-end application-specific integrated circuit (ASIC) designed for beam monitoring applications. The achieved timing resolution of a few nanoseconds enables the measurement of both the luminosity and the beam-induced background. The ASIC, called FBCM23, features six channels with adjustable shaping times, enabling in-field fine-tuning. Each ASIC channel outputs a single binary asynchronous signal encoding time-of-arrival and time-over-threshold information. The FBCM is based on silicon-pad sensors, with two sensor designs presently being considered. This paper presents the results of tests of the FBCM detector prototype using both types of silicon sensors with hadron, muon, and electron beams. Irradiated FBCM23 ASICs and silicon-pad sensors were also tested to simulate the expected conditions near the end of the detector's lifetime in the HL-LHC radiation environment. Based on test results, direct bonding between the sensor and ASIC was chosen, and an optimal bias voltage and ASIC threshold for FBCM operation were proposed. The current design of the front-end test board was validated following the beam test and is now being used for the first front-end module, which is expected to be produced in summer 2025. These results represent a major step forward in validating the FBCM concept, first version of the firmware and establishing a reliable design path for the final detector.
Beam-line instrumentation (beam position and profi↗
Transcript level and sequence determinants of protein abundance and noise in Escherichia coli
The range over which a protein is expressed, and its cell-to-cell variability, is often thought to be linked to the demand for its activity. Steady-state protein level is determined by multiple mechanisms controlling transcription and translation, many of which are limited by DNA- and RNA-encoded signals that affect initiation, elongation and termination of polymerases and ribosomes. We performed a comprehensive analysis of >100 sequence features to derive a predictive model composed of a minimal non-redundant set of factors explaining 66% of the total variation of protein abundance observed in >800 genes in Escherichia coli. The model suggests that protein abundance is primarily determined by the transcript level (53%) and by effectors of translation elongation (12%), whereas only a small fraction of the variation is explained by translational initiation (1%). Our analyses uncover a new sequence determinant, not previously described, affecting translation initiation and suggest that elongation rate is affected by both codon biases and specific amino acid composition. We also show that transcription and translation efficiency may have an effect on expression noise, which is more similar than previously assumed.
59 BASIC BIOLOGICAL SCIENCES↗
Surface plasmon polariton pulse shaping via two-dimensional Bragg grating pairs
Abstract We demonstrate control over the spatial and temporal properties of surface plasmon polaritons (SPPs) launched from nanohole arrays in silver. The arrays provide wave vector matching to allow the conversion of free-space photons into counter-propagating SPPs. SPPs launched from multiple arrays interfere at well-defined spatial positions, and the interference fringes form an all-SPP periodic nano-optical grating which evolves in space and time as the SPPs propagate. The spatio-temporal characteristics of the optical grating can be tuned through various nanohole array parameters such as tilt angle, separation, and array width. In addition, we examine multiperiodic arrays (MPAs) consisting of arrays with different pitches placed adjacent to one another. This platform allows the temporal interference of SPPs with different central wavelengths to be tailored through the MPA geometric and structural parameters. The temporal interference serves as an encoded signal, whereby the frequency components can be controlled by the array properties.
79 ASTRONOMY AND ASTROPHYSICS↗
Shubnikov-de Haas oscillations of biaxial-strain-tuned superconductors in pulsed magnetic field up to 60 T
Two-dimensional (2D) materials have gained increasing prominence not only in fundamental research but also in daily applications. However, to fully harness their potential, it is crucial to optimize their properties with an external parameter and track the electronic structure simultaneously. Magnetotransport over a wide magnetic field range is a powerful method to probe the electronic structure and, for metallic 2D materials, quantum oscillations superimposed on the transport signals encode Fermi surface parameters. In this manuscript, we utilize biaxial strain as an external tuning parameter and investigate the effects of strain on the electronic properties of two quasi-2D superconductors, MoTe 2 and RbV 3 Sb 5 , by measuring their magnetoresistance in pulsed magnetic fields up to 60 T. With a careful selection of insulating substrates, we demonstrate the possibility of both the compressive and tensile biaxial strains imposed on MoTe 2 and RbV 3 Sb 5 , respectively. For both systems, the applied strain has led to superconducting critical temperature enhancement compared to their free-standing counterparts, proving the effectiveness of this biaxial strain method at cryogenic temperatures. Clear quantum oscillations in the magnetoresistance—the Shubnikov–de Haas (SdH) effect—are obtained in both samples. In strained MoTe 2 , the magnetoresistance exhibits a nearly quadratic dependence on the magnetic field and remains non-saturating even at the highest field, whereas in strained RbV 3 Sb 5 , two SdH frequencies showed a substantial enhancement in effective mass values, hinting at a possible enhancement of charge fluctuations. Our results demonstrate that combining biaxial strain and pulsed magnetic field paves the way for studying 2D materials under unprecedented conditions.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Towards verifiable cancer digital twins: tissue level modeling protocol for precision medicine
Cancer exhibits substantial heterogeneity, manifesting as distinct morphological and molecular variations across tumors, which frequently undermines the efficacy of conventional oncological treatments. Developments in multiomics and sequencing technologies have paved the way for unraveling this heterogeneity. Nevertheless, the complexity of the data gathered from these methods cannot be fully interpreted through multimodal data analysis alone. Mathematical modeling plays a crucial role in delineating the underlying mechanisms to explain sources of heterogeneity using patient-specific data. Intra-tumoral diversity necessitates the development of precision oncology therapies utilizing multiphysics, multiscale mathematical models for cancer. This review discusses recent advancements in computational methodologies for precision oncology, highlighting the potential of cancer digital twins to enhance patient-specific decision-making in clinical settings. We review computational efforts in building patient-informed cellular and tissue-level models for cancer and propose a computational framework that utilizes agent-based modeling as an effective conduit to integrate cancer systems models that encode signaling at the cellular scale with digital twin models that predict tissue-level response in a tumor microenvironment customized to patient information. Furthermore, we discuss machine learning approaches to building surrogates for these complex mathematical models. These surrogates can potentially be used to conduct sensitivity analysis, verification, validation, and uncertainty quantification, which is especially important for tumor studies due to their dynamic nature.
60 APPLIED LIFE SCIENCES↗