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At least 73 records · Page 4

Chromosome Model reveals Dynamic Redistribution of DNA Damage into Nuclear Sub-domains

Several proteins involved in the response to DNA double strand breaks (DSB) form microscopically visible nuclear domains, or foci, after exposure to ionizing radiation. Radiation-induced foci (RIF) are believed to be located where DNA damage is induced. To test this assumption, we analyzed the spatial distribution of 53BP1, phosphorylated ATM and gammaH2AX RIF in cells irradiated with high linear energy transfer (LET) radiation. Since energy is randomly deposited along high-LET particle paths, RIF along these paths should also be randomly distributed. The probability to induce DSB can be derived from DNA fragment data measured experimentally by pulsed-field gel electrophoresis. We used this probability in Monte Carlo simulations to predict DSB locations in synthetic nuclei geometrically described by a complete set of human chromosomes, taking into account microscope optics from real experiments. As expected, simulations produced DNA-weighted random (Poisson) distributions. In contrast, the distributions of RIF obtained as early as 5 min after exposure to high LET (1 GeV/amu Fe) were non-random. This deviation from the expected DNA-weighted random pattern can be further characterized by relative DNA image measurements. This novel imaging approach shows that RIF were located preferentially at the interface between high and low DNA density regions, and were more frequent in regions with lower density DNA than predicted. This deviation from random behavior was more pronounced within the first 5 min following irradiation for phosphorylated ATM RIF, while gammaH2AX and 53BP1 RIF showed very pronounced deviation up to 30 min after exposure. These data suggest the existence of repair centers in mammalian epithelial cells. These centers would be nuclear sub-domains where DNA lesions would be collected for more efficient repair.

Costes, Sylvain V.↗

Tensor Decompositions for Count Data that Leverage Stochastic and Deterministic Optimization

There is growing interest to extend low-rank matrix decompositions to multi-way arrays, or tensors. One fundamental low-rank tensor decomposition is the canonical polyadic decomposition (CPD). The challenge of fitting a low-rank, nonnegative CPD model to Poisson-distributed count data is of particular interest. Several popular algorithms use local search methods to approximate the global maximum likelihood estimator from local minima. Simultaneously, a recent trend in theoretical computer science and numerical linear algebra leverages randomization to solve very large, hard problems. The typical approach is to use randomization for a fast approximation and determinism for refinement to yield effective algorithms with theoretical guarantees. Two popular algorithms for Poisson CPD reflect that emergent dichotomy: CP Alternating Poisson Regression is a deterministic algorithm and Generalized Canonical Polyadic decomposition makes use of stochastic algorithms in several variants. This work extends recent work to develop two new methods that leverage randomized and deterministic algorithms for improved accuracy and performance.

97 MATHEMATICS AND COMPUTING↗

Finding the magnetopause location using soft X-ray observations and a statistical inverse method

Variability in the location and shape of the dayside magnetopause is attributed to magnetic reconnection, a fundamental process that enables the transfer of mass, energy, and momentum from the solar wind into the magnetosphere. The spatial and temporal properties of the magnetopause, under varying solar and magnetospheric conditions, remain largely unknown because empirical studies using in-situ observations are challenging to interpret. Global wide field-of-view (FOV) imaging is the only means to simultaneously observe the spatial distribution of the plasma properties over the vast dayside magnetospheric region and, subsequently, quantify the energy transport from the interplanetary medium into the terrestrial magnetosphere. Two upcoming missions, ESA/CAS SMILE and NASA’s LEXI will provide wide-field imagery of the dayside magnetosheath in soft X-rays, an emission generated by charge exchange interactions between high charge-state heavy ions of solar wind origin and exospheric neutral atoms. High-cadence two-dimensional observations of the magnetosheath will allow the estimation of dynamic properties of its inner boundary, the magnetopause, and enable studies of its response to changes in the solar wind dynamic pressure and interplanetary magnetic field orientation. This work introduces a statistically-based estimation approach based on inverse theory to estimate the spatial distribution of magnetosheath soft X-ray emissivities and, with this, identify the location of the magnetopause over the Sun−Earth line. To do so, we simulate the magnetosheath structure using the MHD-based OpenGGCM model and generate synthetic soft X-ray images using LEXI’s orbit and attitude information. Our results show that 3-D estimations using the described statistically-based technique are robust against Poisson-distributed shot noise inherent to soft X-ray images. Also, our proposed methodology shows that the accuracy of both three-dimensional (3-D) estimation and the magnetopause standoff distance calculation highly depends on the observational point.

Gonzalo Cucho-Padin↗

Poisson-response Tensor-on-Tensor Regression and Applications

We introduce Poisson-response tensor-on-tensor regression (PToTR), a novel regression framework designed to handle tensor responses composed element-wise of random Poisson-distributed counts. Tensors, or multi-dimensional arrays, composed of counts are common data in fields such as inter national relations, social networks, epidemiology, and medical imaging, where events occur across multiple dimensions like time, location, and dyads. PToTR accommodates such tensor responses alongside tensor covariates, providing a versatile tool for multi dimensional data analysis. We propose algorithms for maximum likelihood estimation under a canonical polyadic (CP) structure on the regression coefficient tensor that satisfy the positivity of Poisson parameters and then provide an initial theoretical error analysis for PToTR estimators. We also demonstrate the utility of PToTR through three concrete applications: longitudinal data analysis of the Integrated Crisis Early Warning System database, positron emission tomography (PET) image reconstruction, and change-point detection of communication patterns in longitudinal dyadic data. These applications highlight the versatility of PToTR in addressing complex, structured count data across various domains.

97 MATHEMATICS AND COMPUTING↗

Adaptive Load-Balancing Algorithms Using Symmetric Broadcast Networks

In a distributed-computing environment, it is important to ensure that the processor workloads are adequately balanced. Among numerous load-balancing algorithms, a unique approach due to Dam and Prasad defines a symmetric broadcast network (SBN) that provides a robust communication pattern among the processors in a topology-independent manner. In this paper, we propose and analyze three novel SBN-based load-balancing algorithms, and implement them on an SP2. A thorough experimental study with Poisson-distributed synthetic loads demonstrates that these algorithms are very effective in balancing system load while minimizing processor idle time. They also compare favorably with several other existing load-balancing techniques. Additional experiments performed with real data demonstrate that the SBN approach is effective in adaptive computational science and engineering applications where dynamic load balancing is extremely crucial.

Das, Sajal K.↗

Adaptive Load-Balancing Algorithms using Symmetric Broadcast Networks

In a distributed computing environment, it is important to ensure that the processor workloads are adequately balanced, Among numerous load-balancing algorithms, a unique approach due to Das and Prasad defines a symmetric broadcast network (SBN) that provides a robust communication pattern among the processors in a topology-independent manner. In this paper, we propose and analyze three efficient SBN-based dynamic load-balancing algorithms, and implement them on an SGI Origin2000. A thorough experimental study with Poisson distributed synthetic loads demonstrates that our algorithms are effective in balancing system load. By optimizing completion time and idle time, the proposed algorithms are shown to compare favorably with several existing approaches.

Das, Sajal K.↗

Simulation of Crack Propagation in Engine Rotating Components under Variable Amplitude Loading

The crack propagation life of tested specimens has been repeatedly shown to strongly depend on the loading history. Overloads and extended stress holds at temperature can either retard or accelerate the crack growth rate. Therefore, to accurately predict the crack propagation life of an actual component, it is essential to approximate the true loading history. In military rotorcraft engine applications, the loading profile (stress amplitudes, temperature, and number of excursions) can vary significantly depending on the type of mission flown. To accurately assess the durability of a fleet of engines, the crack propagation life distribution of a specific component should account for the variability in the missions performed (proportion of missions flown and sequence). In this report, analytical and experimental studies are described that calibrate/validate the crack propagation prediction capability ]or a disk alloy under variable amplitude loading. A crack closure based model was adopted to analytically predict the load interaction effects. Furthermore, a methodology has been developed to realistically simulate the actual mission mix loading on a fleet of engines over their lifetime. A sequence of missions is randomly selected and the number of repeats of each mission in the sequence is determined assuming a Poisson distributed random variable with a given mean occurrence rate. Multiple realizations of random mission histories are generated in this manner and are used to produce stress, temperature, and time points for fracture mechanics calculations. The result is a cumulative distribution of crack propagation lives for a given, life limiting, component location. This information can be used to determine a safe retirement life or inspection interval for the given location.

Bonacuse, P. J.↗

Simulation of Crack Propagation in Engine Rotating Components Under Variable Amplitude Loading

The crack propagation life of tested specimens has been repeatedly shown to strongly depend on the loading history. Overloads and extended stress holds at temperature can either retard or accelerate the crack growth rate. Therefore, to accurately predict the crack propagation life of an actual component, it is essential to approximate the true loading history. In military rotorcraft engine applications, the loading profile (stress amplitudes, temperature, and number of excursions) can vary significantly depending on the type of mission flown. To accurately assess the durability of a fleet of engines, the crack propagation life distribution of a specific component should account for the variability in the missions performed (proportion of missions flown and sequence). In this report, analytical and experimental studies are described that calibrate/validate the crack propagation prediction capability for a disk alloy under variable amplitude loading. A crack closure based model was adopted to analytically predict the load interaction effects. Furthermore, a methodology has been developed to realistically simulate the actual mission mix loading on a fleet of engines over their lifetime. A sequence of missions is randomly selected and the number of repeats of each mission in the sequence is determined assuming a Poisson distributed random variable with a given mean occurrence rate. Multiple realizations of random mission histories are generated in this manner and are used to produce stress, temperature, and time points for fracture mechanics calculations. The result is a cumulative distribution of crack propagation lives for a given, life limiting, component location. This information can be used to determine a safe retirement life or inspection interval for the given location.

P J Bonacuse↗

Adaptive Detector Arrays for Optical Communications Receivers

The structure of an optimal adaptive array receiver for ground-based optical communications is described and its performance investigated. Kolmogorov phase screen simulations are used to model the sample functions of the focal-plane signal distribution due to turbulence and to generate realistic spatial distributions of the received optical field. This novel array detector concept reduces interference from background radiation by effectively assigning higher confidence levels at each instant of time to those detector elements that contain significant signal energy and suppressing those that do not. A simpler suboptimum structure that replaces the continuous weighting function of the optimal receiver by a hard decision on the selection of the signal detector elements also is described and evaluated. Approximations and bounds to the error probability are derived and compared with the exact calculations and receiver simulation results. It is shown that, for photon-counting receivers observing Poisson-distributed signals, performance improvements of approximately 5 dB can be obtained over conventional single-detector photon-counting receivers, when operating in high background environments.

Vilnrotter, V.↗

A Monte-Carlo Model for the Formation of Radiation-induced Chromosomal Aberrations

Purpose: To simulate radiation-induced chromosome aberrations in mammalian cells (e.g., rings, translocations, and dicentrics) and to calculate their frequency distributions following exposure to DNA double strand breaks (DSBs) produced by high-LET ions. Methods: The interphase genome was assumed to be comprised of a collection of 2 kbp rigid-block monomers following the random-walk geometry. Additional details for the modeling of chromosomal structure, such as chromosomal domains and chromosomal loops, were included. A radial energy profile for heavy ion tracks was used to simulate the high-LET pattern of induced DSBs. The induced DSB pattern depended on the ion charge and kinetic energy, but always corresponded to the DSB yield of 25 DSBs/cell/Gy. The sum of all energy contributions from Poisson-distributed particle tracks was taken to account for all possible one-track and multi-track effects. The relevant output of the model was DNA fragments produced by DSBs. The DSBs, or breakpoints, were defined by (x, y, z, l) positions, where x, y, z were the Euclidian coordinates of a DSB, and where l was the relative position along the genome. Results: The code was used to carry out Monte Carlo simulations for DSB rejoinings at low doses. The resulting fragments were analyzed to estimate the frequencies of specific types of chromosomal aberrations. Histograms for relative frequencies of chromosomal aberrations and P.D.F.s (probability density functions) of a given aberration type were produced. The relative frequency of dicentrics to rings was compared to empirical data to calibrate rejoining probabilities. Of particular interest was the predicted distribution of ring sizes, irrespective of their frequencies relative to other aberrations. Simulated ring sizes were . 4 kbp, which are far too small to be observed experimentally (i.e., by microscopy) but which, nevertheless, are conjectured to exist. Other aberrations, for example, inversions, translocations, as well as multi-centrics were also recorded. Conclusion: High-LET DNA damage affects the frequencies of chromosomal aberrations. The ratio of rings to dicentrics is correct for the genomic size cut-offs corresponding to available experimental data. The present work predicts a relative abundance of small rings following irradiation by heavy ions.

Ponomarev, Artem L.↗

Galactic Cosmic Ray Event-Based Risk Model (GERM) Code

This software describes the transport and energy deposition of the passage of galactic cosmic rays in astronaut tissues during space travel, or heavy ion beams in patients in cancer therapy. Space radiation risk is a probability distribution, and time-dependent biological events must be accounted for physical description of space radiation transport in tissues and cells. A stochastic model can calculate the probability density directly without unverified assumptions about shape of probability density function. The prior art of transport codes calculates the average flux and dose of particles behind spacecraft and tissue shielding. Because of the signaling times for activation and relaxation in the cell and tissue, transport code must describe temporal and microspatial density of functions to correlate DNA and oxidative damage with non-targeted effects of signals, bystander, etc. These are absolutely ignored or impossible in the prior art. The GERM code provides scientists data interpretation of experiments; modeling of beam line, shielding of target samples, and sample holders; and estimation of basic physical and biological outputs of their experiments. For mono-energetic ion beams, basic physical and biological properties are calculated for a selected ion type, such as kinetic energy, mass, charge number, absorbed dose, or fluence. Evaluated quantities are linear energy transfer (LET), range (R), absorption and fragmentation cross-sections, and the probability of nuclear interactions after 1 or 5 cm of water equivalent material. In addition, a set of biophysical properties is evaluated, such as the Poisson distribution for a specified cellular area, cell survival curves, and DNA damage yields per cell. Also, the GERM code calculates the radiation transport of the beam line for either a fixed number of user-specified depths or at multiple positions along the Bragg curve of the particle in a selected material. The GERM code makes the numerical estimates of basic physical and biophysical quantities of high-energy protons and heavy ions that have been studied at the NASA Space Radiation Laboratory (NSRL) for the purpose of simulating space radiation biological effects. In the first option, properties of monoenergetic beams are treated. In the second option, the transport of beams in different materials is treated. Similar biophysical properties as in the first option are evaluated for the primary ion and its secondary particles. Additional properties related to the nuclear fragmentation of the beam are evaluated. The GERM code is a computationally efficient Monte-Carlo heavy-ion-beam model. It includes accurate models of LET, range, residual energy, and straggling, and the quantum multiple scattering fragmentation (QMSGRG) nuclear database.

Cucinotta, Francis A.↗

A Statistician’s Overview of Physics-Informed Neural Networks for Spatio-Temporal Data

The recent success of deep neural network models with physical constraints (so-called, Physics-Informed Neural Networks, PINNs) has led to renewed interest in the incorporation of mechanistic information in predictive models. Statisticians and others have long been interested in this problem, which has led to several practical and innovative solutions dating back decades. In this overview, we focus on the problem of data-driven prediction and inference of dynamic spatio-temporal processes that include mechanistic information, such as would be available from partial differential equations, with a strong focus on the quantification of uncertainty associated with data, process, and parameters. Here, we give a brief review of several paradigms and focus our attention on Bayesian implementations given they naturally accommodate uncertainty quantification. We then show that it is straight-forward to include the Bayesian PINN (B-PINN) within the Bayesian hierarchical model (BHM) framework that has long been considered for modeling dynamic spatio-temporal processes. Such a BHM-PINN is illustrated via a simulation study in which a latent nonlinear Burgers’ equation PDE governs the dynamics of Poisson distributed spatio-temporal data. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work.

Bayesian↗

Event-driven readout development: testing of the EDWARD65P1 chip with integrated event generators

Building on a prototype readout integrated circuit for segmented silicon sensors with the EDWARD event-driven readout architecture, the front-end in each pixel was replaced by a hardware generator to verify readout performance, ensuring no data loss, consistent priority handling, and speed verification. Here, this generator produces Poisson-distributed readout requests with individually tunable rates per pixel via a digitally controlled oscillator. The resulting EDWARD65P1 test ASIC is a 32×32 pixel matrix with a 100 μm pitch, equipped with digital event generators simulating radiation hits at user-defined rates. Test results for this new design are presented.

47 OTHER INSTRUMENTATION↗

Measuring the X-ray luminosities of DESI groups from eROSITA Final Equatorial-Depth Survey – I. X-ray luminosity–halo mass scaling relation

ABSTRACT We use the eROSITA Final Equatorial-Depth Survey (eFEDS) to measure the rest-frame 0.1–2.4 keV band X-ray luminosities of ∼600 000 DESI groups using two different algorithms in the overlap region of the two observations. These groups span a large redshift range of 0.0 ≤ zg ≤ 1.0 and group mass range of $10^{10.76}\, h^{-1}\, \mathrm{M}_{\odot } \le M_h \le 10^{15.0}\, h^{-1}\, \mathrm{M}_{\odot }$. (1) Using the blind detection pipeline of eFEDS, we find that 10932 X-ray emission peaks can be cross-matched with our groups, ∼38 per cent of which have a signal-to-noise ratio $\rm {S}/\rm {N} \ge 3$ in X-ray detection. Comparing to the numbers reported in previous studies, this matched sample size is a factor of ∼6 larger. (2) By stacking X-ray maps around groups with similar masses and redshifts, we measure the average X-ray luminosity of groups as a function of halo mass in five redshift bins. We find that in a wide halo mass range, the X-ray luminosity, LX, is roughly linearly proportional to Mh and quite independent to the redshift of the groups. (3) We use a Poisson distribution to model the X-ray luminosities obtained using two different algorithms and obtain the best-fit $L_{\rm X}=10^{28.46\pm 0.03}M_{\rm h}^{1.024\pm 0.002}$ and $L_{\rm X}=10^{26.73 \pm 0.04}M_{\rm h}^{1.140 \pm 0.003}$ scaling relations, respectively. The best-fit slopes are flatter than the results previously obtained but closer to a self-similar prediction.

Astronomy & Astrophysics↗

Extended nonergodic regime and spin subdiffusion in disordered SU(2)-symmetric Floquet systems

In this work, we explore thermalization and quantum dynamics in a one-dimensional disordered SU(2)-symmetric Floquet model, where a many-body localized phase is prohibited by the non-Abelian symmetry. Despite the absence of localization, we find an extended nonergodic regime at strong disorder where the system exhibits nonthermal behaviors. In the strong disorder regime, the level spacing statistics exhibit neither a Wigner-Dyson nor a Poisson distribution, and the spectral form factor does not show a linear-in-time growth at early times characteristic of random matrix theory. The average entanglement entropy of the Floquet eigenstates is subthermal, although violating an area-law scaling with system sizes. We further compute the expectation value of local observables and find strong deviations from the eigenstate thermalization hypothesis. The infinite-temperature spin autocorrelation function decays at long times as $t^{–β}$ with $\textit{β}$ < 0.5, indicating subdiffusive transport at strong disorders.

36 MATERIALS SCIENCE↗

Constraints from isoscaling on the source size in energetic heavy ion collisions

In the framework of the statistical multifragmentation model, the nuclear isoscaling analysis is extended to constrain the ratio between the sizes of the decaying sources formed in a collision between two heavy ions. It is found that the ratio between the probabilities of observing n fragments in each event, for each of the sources, follows a scaling law, similar to the traditional nuclear isoscaling. However, the corresponding slope is sensitive to the source sizes. This property is explained analytically using the grand-canonical ensemble. Furthermore, the extent to which our findings are affected by finite size effects and by the deexcitation of the hot primary fragments is investigated. The scaling turns out to be robust and weakly affected by effects implied by these two aspects. We also find that the Poisson distribution is a fairly good approximation to the above mentioned probabilities, associated with both the primordial fragments, produced at the breakup stage, and the final ones, found at the end of the fragment deexcitation process.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Quantum chaos, integrability, and late times in the Krylov basis

Quantum chaotic systems are conjectured to display a spectrum whose fine-grained features (gaps and correlations) are well described by random matrix theory (RMT). We propose and develop a complementary version of this conjecture: quantum chaotic systems display a Lanczos spectrum whose local means and covariances are well described by RMT. To support this proposal, we first demonstrate its validity in examples of chaotic and integrable systems. We then show that for Haar-random initial states in RMTs the mean and covariance of the Lanczos spectrum suffice to produce the full long-time behavior of general survival probabilities including the spectral form factor, as well as the spread complexity. In addition, for initial states with continuous overlap with energy eigenstates, we analytically find the long-time averages of the probabilities of Krylov basis elements in terms of the mean Lanczos spectrum. This analysis suggests a notion of eigenstate complexity, the statistics of which differentiate integrable systems and classes of quantum chaos. Lastly, we clarify the relation between spread complexity and the universality classes of RMT by exploring various values of the Dyson index and Poisson distributed spectra.

Combinatorics↗

Q-BEEP: Quantum Bayesian Error Mitigation Employing Poisson Modeling over the Hamming Spectrum

Quantum computing technology has grown rapidly in recent years, with new technologies being explored, error rates being reduced, and quantum processor’s qubit capacity growing. However, near-term quantum algorithms are still unable to be induced without compounding consequential levels of noise, leading to non-trivial erroneous results. Quantum Error Correction (in-situ error mitigation) and Quantum Error Mitigation (post-induction error mitigation) are promising fields of research within the quantum algorithm scene, aiming to alleviate quantum errors, increasing the overall fidelity and hence the overall quality of circuit induction. Earlier this year, a pioneering work, namely HAMMER, published in ASPLOS-22 demonstrated the existence of a latent structure regarding post-circuit induction errors when mapping to the Hamming spectrum. However, they intuitively assumed that errors occur in local clusters, and that at higher average Hamming distances this structure falls away. In this work, we show that such a correlation structure is not only local but extends certain non-local clustering patterns which can be precisely described by a Poisson distribution model taking the input circuit, the device run time status (i.e., calibration statistics) and qubit topology into consideration. Using this quantum error characterizing model, we developed an iterative algorithm over the generated Bayesian network state-graph for post-induction error mitigation. Thanks to more precise modeling of the error distribution latent structure and the new iterative method, our Q-Beep approach provides state of the art performance and can boost circuit execution fidelity by up to 234.6% on Bernstein-Vazirani circuits and on average 71.0% on QAOA solution quality, using 16 practical IBMQ quantum processors. For other benchmarks such as those in QASMBench, the fidelity improvement is up to 17.8%. Q-Beep is a light-weight post-processing technique that can be performed offline and remotely, making it a useful tool for quantum vendors to integrate and provide more reliable circuit induction results.

Stein, Samuel A.↗