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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Globally optimal interferometry with lossy twin Fock probes

Parity or quadratic spin (e.g., J z 2 ) readouts of a Mach–Zehnder (MZ) interferometer probed with a twin Fock (TF) input state allow saturating the optimal sensitivity attainable among all mode-separable states with a fixed total number of particles but only when the interferometer phase θ is near zero. When more general Dicke state probes are used, the parity readout saturates the quantum Fisher information (QFI) at θ = 0, whereas better-than-standard quantum limit performance of the J z 2 readout is restricted to an o ( N ) occupation imbalance. We show that a method of moments readout of two quadratic spin observables J z 2 and J + 2 + J − 2 is globally optimal for Dicke state probes; i.e., the error saturates the QFI for all θ . In the lossy setting, we derive the time-inhomogeneous Markov process describing the effect of particle loss on TF states, showing that the method of moments readout of four at-most-quadratic spin observables is sufficient for globally optimal estimation of θ when two or more particles are lost. The analysis culminates in a numerical calculation of the QFI matrix for distributed MZ interferometry on the four-mode state | N 4 , N 4 , N 4 , N 4 〉 and its lossy counterparts, showing that an advantage for the estimation of any linear function of the local MZ phases θ 1 and θ 2 (compared to independent probing of the MZ phases by two copies of | N 4 , N 4 〉 ) appears when more than one particle is lost.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

HDSense: An efficient method for ranking observable sensitivity

Identifying which observables most effectively constrain model parameters can be computationally prohibitive when considering full likelihoods of many correlated observables. This is especially important for, e.g., hadronization models, where high precision is required to interpret the results of collider experiments. We introduce the High-Dimensional Sensitivity (HDSense) score, a computationally efficient metric for ranking observable sets using only one-dimensional histograms. Derived by profiling over unknown correlations in the Fisher information framework, the score balances total information content against redundancy between observables. We apply HDSense to rank a set observables in terms of their constraining power with respect to five parameters of the Lund string model of hadronization implemented in Pythia using simulated leptonic collider events at the $Z$ pole. Validation against machine-learning--based full-likelihood approximations demonstrates that HDSense successfully identifies near-optimal observable subsets. The framework naturally handles data from multiple experiments with different acceptances and incorporates detector effects. While demonstrated on hadronization models, the methodology applies broadly to generic parameter estimation problems where correlations are unknown or difficult to model.

Assi, Benoît [Cincinnati U.] (ORCID:00000003092433↗
DOE OSTI2026

Entanglement Requirements for Coherent Enhancement in Detectors

Coherent enhancement is a powerful mechanism for improving the sensitivity of a wide range of detectors, but its practical use is often limited by the difficulty of preparing the required quantum states. We show that this difficulty has a fundamental origin: coherent enhancement of a signal interacting with a detector is quantitatively constrained by entanglement. We prove general bounds on how the strength of coherent effects can scale with system size, as a function of the single-mode entanglement entropy of the detector. These bounds smoothly interpolate between the incoherent and fully coherent regimes, and apply both to parameter-estimation problems and to scattering processes. We discuss these results from two complementary perspectives: First, they appear as bounds on the quantum Fisher information of many-body states, which translate directly into limits on parameter sensitivity via the quantum Cramér-Rao bound. Second, they can be interpreted as limits on a class of scattering cross sections, leading to predictions for how minimum detectable interaction strengths scale with target size. Together, these results provide a unified view of coherent enhancement in metrology and scattering experiments, and motivate the development of new techniques for generating entangled detector states.

Bogorad, Zachary [Fermilab] (ORCID:000000019913647↗
DOE OSTI2024

Measure this, not that: Optimizing the cost and model-based information content of measurements

Model-based design of experiments (MBDoE) is a powerful framework for selecting and calibrating science-based mathematical models from data. Here, this work extends popular MBDoE workflows by proposing a convex mixed integer (non)linear programming (MINLP) to optimize the selection of measurements. The solver MindtPy is modified to support calculating the D-optimality objective and its gradient via an external package, scipy, using the grey-box module in Pyomo. The new approach is demonstrated in two case studies: estimating highly correlated kinetics from a batch reactor and estimating transport parameters in a large-scale rotary packed bed for CO 2 capture. Both case studies show how examining the Pareto optimal trade-offs between information content measured by A- and D-optimality versus measurement budget offers practical guidance for selecting measurements for scientific experiments.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Stochastic Waveform Estimation at the Fundamental Quantum Limit

Although measuring the deterministic waveform of a weak classical force is a well-studied problem, estimating a random waveform, such as the spectral density of a stochastic signal field, is much less well understood despite it being a widespread task at the frontier of experimental physics. State-of-the-art precision sensors of random forces must account for the underlying quantum nature of the measurement but the optimal quantum protocol for interrogating such linear sensors is not known. We derive the fundamental precision limit: the extended-channel quantum Cramér-Rao bound. In the experimentally relevant regime in which losses dominate, we prove that non-Gaussian-state preparation and measurement are required to achieve this fundamental limit and we determine numerically the optimal non-Gaussian protocol. We discuss how this scheme could accelerate searches for signatures of quantum gravity, stochastic gravitational waves, and axionic dark matter.

Axions↗
DOE OSTI2025

Noise Constraints on Sensitivity Scaling in Quantum Nonlinear Metrology

Quantum-enhanced metrology surpasses classical metrology by improving estimation precision scaling with a resource 𝑁 (e.g., particle number or energy) from 1/√𝑁 to 1/𝑁. Through the use of nonlinear effects, Roy and Braunstein [Exponentially enhanced quantum metrology, Phys. Rev. Lett. 100, 220501 (2008)] derived a 1/𝑁 2 scaling. However, later works argued this exponential improvement is unphysical and that even modest gains, like 1/𝑁 2 , may vanish under noise. We show that, in the presence of small errors, the nonlinear interactions enabling metrological enhancement induce emergent errors. Here, the errors propagate through the sensing protocol and are magnified proportional to any intended nonlinear enhancement. We identify a critical value of the parameter to be estimated, for a fixed error, below which the emergent errors can be avoided.

Quantum Fisher information↗
DOE OSTI2022

Transmission estimation at the quantum Cramér-Rao bound with macroscopic quantum light

The field of quantum metrology seeks to apply quantum techniques and/or resources to classical sensing approaches with the goal of enhancing the precision in the estimation of a parameter beyond what can be achieved with classical resources. Theoretically, the fundamental minimum uncertainty in the estimation of a parameter for a given probing state is bounded by the quantum Cramér-Rao bound. From a practical perspective, it is necessary to find physical measurements that can saturate this fundamental limit and to show experimentally that it is possible to perform measurements with the required precision to do so. Here we perform experiments that saturate the quantum Cramér-Rao bound for transmission estimation over a wide range of transmissions when probing the system under study with a continuous wave bright two-mode squeezed state. To properly take into account the imperfections in the generation of the quantum state, we extend our previous theoretical results to incorporate the measured properties of the generated quantum state. For our largest transmission level of 84%, we show a 62% reduction over the optimal classical protocol in the variance in transmission estimation when probing with a bright two-mode squeezed state with -8 dB of intensity-difference squeezing. Given that transmission estimation is an integral part of many sensing protocols, such as plasmonic sensing, spectroscopy, calibration of the quantum efficiency of detectors, etc., the results presented promise to have a significant impact on a number of applications in various fields of research.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Forecasts on the Dark Matter Density Profiles of Dwarf Spheroidal Galaxies with Current and Future Kinematic Observations

We forecast parameter uncertainties on the mass profile of a typical Milky Way dwarf spheroidal galaxy (dSph) using the spherical Jeans equation and Fisher matrix formalism. For a Draco-like system we show that radial velocity measurements for 1000 individual stars can constrain the mass contained within the effective radius of a dSph to within 5%. This is consistent with constraints extracted from current observational data. We compare two systems, a cusp and core, and demonstrate that a minimum sample of 100,000 (10,000) stars with both radial and proper motions measurements is required to disentangle their inner slopes at the 2σ (1σ) level. If using the log-slope measured at the half-light radius as a proxy for differentiating between a core or cusp slope, only 1000 line-of-sight and proper motions measurements are required; however, we show this choice of radius does not always unambiguously differentiate between core and cusped profiles. Once observational errors are below half the value of the intrinsic dispersion, improving the observational precision yields little change in the density profile uncertainties. The choice of priors in our profile shape analysis plays a crucial role when the number of stars in a system is less than 100 but does not affect the resulting uncertainties for larger kinematic samples. Our predicted 2D confidence regions agree well with those from a full likelihood analysis run on a mock kinematic data set taken from the Gaia Challenge, validating our Fisher predictions. Our methodology is flexible, allowing us to predict density profile uncertainties for a wide range of current and future kinematic data sets.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Capturing non-Gaussianity of the large-scale structure with weighted skew-spectra

The forthcoming generation of wide-field galaxy surveys will probe larger volumes and galaxy densities, thus allowing for a much larger signal-to-noise ratio for higher-order clustering statistics, in particular the galaxy bispectrum. Extracting this information, however, is more challenging than using the power spectrum due to more complex theoretical modeling, as well as significant computational cost of evaluating the bispectrum signal and the error budget. To overcome these challenges, several proxy statistics have been proposed in the literature, which partially or fully capture the information in the bispectrum, while being computationally less expensive than the bispectrum. One such statistics are weighted skew-spectra, which are cross-spectra of the density field and appropriately weighted quadratic fields. Using Fisher forecasts, we show that the information in these skew-spectra is equivalent to that in the bispectrum for parameters that appear as amplitudes in the bispectrum model, such as galaxy bias parameters or the amplitude of primordial non-Gaussianity. We consider three shapes of the primordial bispectrum: local, equilateral and that due to massive particles with spin two during inflation. In conclusion, to obtain constraints that match those from a measurement of the full bispectrum, we find that it is crucial to account for the full covariance matrix of the skew-spectra.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Photo-z outlier self-calibration in weak lensing surveys

Calibrating photometric redshift errors in weak lensing surveys with external data is extremely challenging. In this work, we show that both Gaussian and outlier photo-z parameters can be self-calibrated from the data alone. This comes at no cost for the neutrino masses, curvature and dark energy equation of state w0, but with a 65% degradation when both w0 and wa are varied. We perform a realistic forecast for the Vera Rubin Observatory (VRO) Legacy Survey of Space and Time (LSST) 3× 2 analysis, combining cosmic shear, projected galaxy clustering and galaxy - galaxy lensing. We confirm the importance of marginalizing over photo-z outliers. We examine a subset of internal cross-correlations, dubbed "null correlations", which are usually ignored in 3× 2 analyses. Despite contributing only ~ 10% of the total signal-to-noise, these null correlations improve the constraints on photo-z parameters by up to an order of magnitude. Using the same galaxy sample as sources and lenses dramatically improves the photo-z uncertainties too. Together, these methods add robustness to any claim of detected new Physics, and reduce the statistical errors on cosmology by 15% and 10% respectively. Finally, including CMB lensing from an experiment like Simons Observatory or CMB-S4 improves the cosmological and photo-z posterior constraints by about 10%, and further improves the robustness to systematics. To give intuition on the Fisher forecasts, we examine in detail several toy models that explain the origin of the photo-z self-calibration. Our Fisher code LaSSI (Large-Scale Structure Information), which includes the effect of Gaussian and outlier photo-z, shear multiplicative bias, linear galaxy bias, and extensions to LCDM, is publicly available at \href{https://github.com/EmmanuelSchaan/LaSSI}{https://github.com/EmmanuelSchaan/LaSSI}.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Ultra High Performance Liquid Chromatography with Quadrupole Time-of-Flight Mass Spectrometry and Fisher Ratio Analysis for Discovery-Based Analysis

The ability to discover minute differences between samples or sample classes for ultrahigh performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UHPLC-QTOF) can be a challenging endeavor especially when these differences are not known a priori. Indeed a typical UHPLC-QTOF analysis time of ~15 minutes can generate over 4 gigabytes of information for a single sample. Implementation of chemometrics such as Fisher ratio (F-ratio) analysis will allow the analyst to quickly and precise probe the chemical differences between different samples or sample classes. F-ratio analysis can be used to find sample or sample class distinguishing compounds reducing the 5 gigabytes of information into a simple, yet informative hit list. Moreover through combinatorial rearrangement, it is possible to determine a F-ratio threshold to separate the real and non-real hits. The F-ratio software presented herein is a semi-automated algorithm that processes the raw, exported .csv files from the SCIEX 500R QTOF in as little as 30 seconds. While further research is needed to modify and perfect the software to deal with high resolution mass spectra precise to 0.0001 Daltons, the current software, precise to 0.1 Da, is able to find significant chemical differences despite some of them being at extremely low concentrations nearing the limit of detection.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Cosmology with persistent homology: a Fisher forecast

Abstract Persistent homology naturally addresses the multi-scale topological characteristics of the large-scale structure as a distribution of clusters, loops, and voids. We apply this tool to the dark matter halo catalogs from theQuijotesimulations, and build a summary statistic for comparison with the joint power spectrum and bispectrum statistic regarding their information content on cosmological parameters and primordial non-Gaussianity. Through a Fisher analysis, we find that constraints from persistent homology are tighter for 8 out of the 10 parameters by margins of 13–50%. The complementarity of the two statistics breaks parameter degeneracies, allowing for a further gain in constraining power when combined. We run a series of consistency checks to consolidate our results, and conclude that our findings motivate incorporating persistent homology into inference pipelines for cosmological survey data.

Astronomy & Astrophysics↗
DOE OSTI2022

Implications of the correlation between bulge-to-total baryonic mass ratio and the number of satellites for SAGA galaxies

We searched for correlations between the number of satellites and fundamental galactic properties for the Milky Way-like host galaxies in order to better understand their diverse satellite populations. We specifically aim to understand why galaxies that are very similar in stellar mass content, star formation rate, and local environment have very different numbers of satellites. Deep and extensive spectroscopic observations are needed to characterize the complete satellite luminosity function beyond the Local Group. One such endeavor is an ongoing Satellites of Galactic Analogs (SAGA) spectroscopic survey that has completed spectroscopic observations of 36 Milky Way-like galaxies within their virial radii down to the luminosity of Leo I dwarf galaxy. We correlated the number of satellites of SAGA galaxies with several fundamental properties of their hosts – including total specific angular momentum, which is considered to be well preserved throughout galaxy lifetime – in an attempt to identify the main driver of their diverse satellite populations. We aim to reveal some intrinsic galactic property decisive in making more or less satellites irrespective of baryonic mass or the environment in which galaxies reside. We modeled Spitzer Heritage Archive images of SAGA host galaxies at 3.6 and 4.5 microns with GALFIT code to obtain their stellar masses. We also searched the Extragalactic Database for information on their gas content and rotation velocities. Empirical correlations, like the baryonic Tully–Fisher relation and the stellar mass–size relation were used to exclude outliers. All the available galactic properties from the literature along with measured stellar masses were correlated with the number of satellites and no significant correlation was found. However, when we considered the “expected” number of satellites based on the correlation between the baryonic bulge-to-total ratio and the number of satellites confirmed for several nearby galaxies then strong correlations emerge between this number and (1) the mass of the bulge, and (2) the total specific angular momentum. The first correlation is positive, implying that galaxies with more massive bulges have more satellites, as already confirmed. Furthermore, the second correlation with the angular momentum is negative, meaning that, the smaller the angular momentum, the greater the number of expected satellites. This would imply that either satellites cannot form if galaxy angular momentum is too high, or that satellites form inside-out, so that angular momentum is being transferred to the outer parts of the galaxies. However, deeper spectroscopic observations are needed to confirm these findings, because they rely on the expected rather than detected number of satellites. There was a luminosity limit to the SAGA survey equivalent to the luminosity of Leo I dwarf satellite of the Milky Way galaxy (the SAGA limit). In particular, correlations found in this work are very susceptible to the total number of satellites of the NGC 4158 galaxy. This galaxy is predicted to have many more satellites than detected up to the SAGA limit.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Evolution and Trends of Industrial Control System Cyber Incidents since 2017

The industrial control systems (ICSs) that manage our critical infrastructure are increasingly converging with corporate networks and the Internet as technology and businesses prioritize digital connectivity. These connections make them more vulnerable and available to malicious cyber actors who traditionally targeted the companies’ more public-facing information technology (IT) networks. This paper will review select publicly reported cyber incidents to highlight the continued and growing threat to ICS devices and operational technology (OT) environments. It will summarize the incident and when available, will provide information on the cyber actors, the vulnerabilities they exploited, and any publications the U.S. Government (USG) provided in response. Data belonging to the Department of Homeland Security (DHS) will be used to highlight quantitative trends concerning ICS incidents. This paper builds on “History of Industrial Control System Cyber Incidents” (Hemsley & Fisher 2018), a paper that highlighted select noteworthy threats and incidents to ICS systems up to 2017. This paper will similarly review select incidents occurring after the last previously reviewed incident, Triton/HatMan, December 2017, and will note ICS incident trends including IT/OT convergence and advances in cyber-threat actors’ capabilities in observed in the examined incidents.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2021

Effects of overlapping sources on cosmic shear estimation: Statistical sensitivity and pixel-noise bias

The next generation of dark-energy imaging surveys — so called “Stage-IV” surveys, such as that of the Rubin Observatory Legacy Survey of Space and Time (LSST) — will cross a threshold in the number density of detected sources on the sky that requires qualitatively different image analysis and measurement techniques compared to the current generation of Stage-III surveys. In Stage-IV surveys, a significant amount of the cosmologically useful information is due to sources whose images overlap with those of other sources on the sky. Here, we focus on the weak gravitational lensing probe, for which we expect the largest impact since the cosmic shear signal is primarily encoded in the estimated shapes of observed galaxies and thus directly impacted by overlaps. We introduce a framework based on the Fisher formalism to analyze the effect of the overlapping sources (“blending”) on the estimation of cosmic shear. This method gives concrete predictions for the minimum loss of information due to noise and blending for any choice of “deblending” scheme and shape-measurement algorithm. Our studies account for undetected sources but do not address their full effects and biases they may introduce. We use simulated images and predict this impact of blending for three surveys: the Dark Energy Survey (DES), the Hyper-Suprime Cam Subaru Strategic Program (HSC-SSP), and the Rubin LSST. Our methodology successfully estimates the statistical sensitivity to weak lensing for DES and HSC early results. For LSST, we present the expected loss in statistical sensitivity for the ten-year survey due to blending. We find that for approximately 62% of galaxies that are likely to be detected in full-depth LSST images, at least 1% of the flux in their pixels is from overlapping sources. We also find that the statistical correlations between measures of overlapping galaxies and, to a much lesser extent (0.2%) the higher shot noise level due to their presence, decrease the effective number density of galaxies, N eff , by ~ 18%. We calculate an upper limit on N eff of 39.4 galaxies per arcmin 2 in r band. We study the impact of stars on as a function of stellar density and illustrate the diminishing returns of extending the survey into lower Galactic latitudes. We extend the simulation-based Fisher formalism to predict the expected increase in pixel-noise bias due to blending for maximum-likelihood (ML) shape estimators. We find that noise bias depends sensitively on the particular shape estimator and measure of ensemble-average shape that is used, and properties of the galaxy that include redshift-dependent quantities such as size and luminosity. The source code for these studies is available online.[The documented software developed for the catalog-level studies are available in the open-source LSST DESC github repository https://github.com/LSSTDESC/WeakLensingDeblending. The software for analyzing one or two galaxies with user-defined parameters is in the open-source github repository https://github.com/ismael-mendoza/ShapeMeasurementFisherFormalism.]

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Use of Fisher's Ratio assisted multivariate curve resolution- alternating least squares for discovery-based analysis using ultrahigh pressure liquid chromatography-high resolution mass spectrometry

Non-targeted analysis of complex chemical mixtures can be difficult considering the convoluted nature of the matrix and the potential unknown chemical differences between samples or classes of samples. Ultrahigh pressure liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UHPLC-QTOF) is an ideal technique to probe chemical differences for a wide variety of samples. While UHPLC-QTOF can discover minute chemical differences down to low part per billion (ppb) concentrations with a high degree of confidence, the application of high-resolution mass spectrometry can yield massive amounts of information (∼ 10 gb per sample) that cannot be analyzed manually. Therefore, the application of chemometric techniques is mandatory for the interrogation of complex samples. Fisher's ratio (FR) assisted multivariate curve resolution-alternating least squares (MCR-ALS) was used to the discover and identify the chemical differences between two classes of materials: 1) a pond water matrix and 2) the matrix spiked with a pharmaceutical standard mix containing 17 compounds. Thirteen of the seventeen spiked compounds were discovered using FR analysis, and then five were successfully deconvoluted using MCR-ALS wherein the number of curves chosen were automatically determined using singular value decomposition (SVD). In conclusion, the use of an automated FR assisted MCR-ALS will aid in discovering trace levels of chemical components without the need for the researcher to provide potentially biased input which will aid in non-targeted workflow.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Joint velocity and density reconstruction of the Universe with nonlinear differentiable forward modeling

Reconstructing the initial conditions of the Universe from late-time observations has the potential to optimally extract cosmological information. Due to the high dimensionality of the parameter space, a differentiable forward model is needed for convergence, and recent advances have made it possible to perform reconstruction with nonlinear models based on galaxy (or halo) positions. In addition to positions, future surveys will provide measurements of galaxies' peculiar velocities through the kinematic Sunyaev-Zel'dovich effect (kSZ), type Ia supernovae, the fundamental plane relation, and the Tully-Fisher relation. Here we develop the formalism for including halo velocities, in addition to halo positions, to enhance the reconstruction of the initial conditions. We show that using velocity information can significantly improve the reconstruction accuracy compared to using only the halo density field. Here we study this improvement as a function of shot noise, velocity measurement noise, and angle to the line of sight. We also show how halo velocity data can be used to improve the reconstruction of the final nonlinear matter overdensity and velocity fields. We have built our pipeline into the differentiable Particle-Mesh FlowPM package, paving the way to perform field-level cosmological inference with joint velocity and density reconstruction. This is especially useful given the increased ability to measure peculiar velocities in the near future.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Assessment of human nuclear and mitochondrial DNA qPCR assays for quantification accuracy utilizing NIST SRM 2372a

In forensic DNA casework, a highly accurate real-time quantitative polymerase chain reaction (qPCR) assay is recommended per the Scientific Working Group on DNA Analysis Methods (SWGDAM) (SWGDAM Validation Guidelines for DNA Analysis Methods [1]) to determine whether a DNA sample is of sufficient quantity and robust quality to move forward with downstream short tandem repeats (STR) or sequencing analyses. Most of these assays rely on a standard curve, referred to herein and traditionally as absolute qPCR, in which an unknown is compared, relative to that curve. However, one fundamental issue with absolute qPCR is the quantifiable concentration of commercial assay standards can vary depending on (1) origin, i.e., whether from a cell line or a human subject, (2) supplier, (3) lot number, (4) shipping method, etc. In 2018, the National Institute for Standards and Technology (NIST) released a human DNA standard reference material for evaluating qPCR quantification standards, Standard Reference Material (SRM) 2372a, Romsos et al. (2018) [2] which contains three well-characterized human genomic DNA samples: Component A) a single male1 donor, Component B) a single female 1 donor, and Component C) a 1:3 male 2 :female 2 donor, each with certification data for nDNA and informational mitochondrial DNA(mtDNA)/nuclear DNA (nDNA) ratio data. The SRM 2372a was used to assess four qPCR assays: (1) Quantifiler Trio (Thermo Fisher Scientific, Waltham, MA) for nDNA quantification, (2) NovaQUANT (EMD Millipore Corporation, San Diego, CA) for nDNA and mtDNA quantification, (3) a custom duplex mtDNA assay, and (4) a custom triplex mtDNA assay. Additionally, extracts from eighteen (18) skeletal remains were tested with the latter three assays for concordance of DNA concentration and with assays (2) and (3), for the degradation state. Our assessment revealed that an accurate, efficient, and reproducible qPCR assay is dependent on (1) the quality and reliability of the DNA standard, (2) the qPCR chemistry, and (3) the specific primers, and probes (if applicable), used in an assay. Finally, our findings indicate qPCR assays may not always quantify as expected and that performance of each lot should be verified using a well-characterized DNA standard such as the NIST SRM 2372a and adjusted if warranted.

59 BASIC BIOLOGICAL SCIENCES↗