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DOE OSTI2021

Blinking statistics and molecular counting in direct stochastic reconstruction microscopy (dSTORM)

Abstract Motivation Many recent advancements in single-molecule localization microscopy exploit the stochastic photoswitching of fluorophores to reveal complex cellular structures beyond the classical diffraction limit. However, this same stochasticity makes counting the number of molecules to high precision extremely challenging, preventing key insight into the cellular structures and processes under observation. Results Modelling the photoswitching behaviour of a fluorophore as an unobserved continuous time Markov process transitioning between a single fluorescent and multiple dark states, and fully mitigating for missed blinks and false positives, we present a method for computing the exact probability distribution for the number of observed localizations from a single photoswitching fluorophore. This is then extended to provide the probability distribution for the number of localizations in a direct stochastic optical reconstruction microscopy experiment involving an arbitrary number of molecules. We demonstrate that when training data are available to estimate photoswitching rates, the unknown number of molecules can be accurately recovered from the posterior mode of the number of molecules given the number of localizations. Finally, we demonstrate the method on experimental data by quantifying the number of adapter protein linker for activation of T cells on the cell surface of the T-cell immunological synapse. Availability and implementation Software and data available at https://github.com/lp1611/mol_count_dstorm. Supplementary information Supplementary data are available at Bioinformatics online.

Patel, Lekha↗

DOE OSTI2023

Searching for heavy leptophilic Z′: from lepton colliders to gravitational waves

Abstract We study the phenomenology of leptophilicZ′ gauge bosons at the future high-energye + e − andμ + μ − colliders, as well as at the gravitational wave observatories. The leptophilicZ′ model, although well-motivated, remains largely unconstrained from current low-energy and collider searches forZ′ masses above$$ \mathcal{O} $$ O (100 GeV), thus providing a unique opportunity for future lepton colliders. Taking$$ \textrm{U}{(1)}_{L_{\alpha }-{L}_{\beta }} $$ U 1 L α − L β (α,β=e,μ,τ) models as concrete examples, we show that futuree + e − andμ + μ − colliders with multi-TeV center-of-mass energies provide unprecedented sensitivity to heavy leptophilicZ′ bosons. Moreover, if these U(1) models are classically scale-invariant, the phase transition at the U(1) symmetry-breaking scale tends to be strongly first-order with ultra-supercooling, and leads to observable stochastic gravitational wave signatures. We find that the future sensitivity of gravitational wave observatories, such as advanced LIGO-VIRGO and Cosmic Explorer, can be complementary to the collider experiments, probing higherZ′ masses up to$$ \mathcal{O} $$ O (10 4 TeV), while being consistent with naturalness and perturbativity considerations.

Physics↗

DOE OSTI2021

L-H transition trigger physics in ITER-similar plasmas with applied n = 3 magnetic perturbations

The L–H transition power threshold PLH is observed to increase with applied n = 3 resonant magnetic perturbations (RMP) in ITER-similar-shape plasmas with balanced neutral beam torque injection in DIII-D. The increase is most pronounced with added electron–cyclotron heating: PLH increases with decreasing edge plasma collisionality as PLH/PLH-08 ~ (ν*)−0.5, where PLH-08 is the 2008 ITPA multi-machine power threshold scaling. This result raises concerns for H-mode access at low edge collisionality in ITER, where RMP may have to be applied before the L–H transition to safely suppress the first edge-localized mode. Non-axisymmetric modifications with RMP include a simultaneous reduction of the radial electric field (Er) well depth and E × B shear. This can be attributed to increasing edge toroidal co-current rotation, and is consistent with substantially increased local long-wavelength turbulence (measured via beam emission spectroscopy). At high RMP perturbation strength the edge electric field Er reverses sign locally (becomes positive), with changes in dominant turbulence modes. Edge magnetic stochasticity provides an attractive explanation of the observed modifications, and the observed changes in toroidal rotation and Er are consistent with a simple fluid model describing radial electron current flow along stochastic fieldlines. The observed collisionality dependence of the L-mode edge electric field with applied RMP is also qualitatively consistent with this model. Reflectometry data indicate a significant reduction of the normalized L-mode radial density gradient a/Ln at high RMP field with simultaneous increase in radial particle flux and electron thermal flux from power balance analysis. We conjecture that the increase of PLH with RMP results from the combined effects of reduced E × B flow shear (increasing turbulent transport levels) and toroidal/poloidal flow modulation due to edge stochasticity. Initial experiments indicate that non-resonant n = 3 magnetic perturbations lead only to relatively small changes in Er, E × B shear and fluctuation characteristics, and have less impact on the L–H transition power threshold. This motivates further exploration of the RMP spectrum dependence of PLH for possible mitigation of the observed threshold increase.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Thermally induced mimicry of quantum cluster excitations and implications for the magnetic transition in FePSe 3

In two dimensional magnets, the interplay of thermal fluctuations and spin anisotropy control the existence of long-range magnetic order. In the van der Waals antiferromagnets FePX 3 , orbital degeneracy in the 𝑡 2⁢𝑔 levels of the Fe 2+ ions in octahedral coordination yields strong uniaxial anisotropy, which stabilizes magnetic order up to 𝑇 ≈ 100 K. Recent inelastic neutron scattering measurements around the magnetic ordering transition have shown the existence of a broad spectrum of magnetic fluctuations with nontrivial momentum dependence, which has been interpreted as evidence for localized entangled cluster excitations. In this paper, we offer an alternative interpretation using classical nonlinear spin dynamics simulations. We present stochastic Landau Lifshitz dynamics simulations that reproduce the neutron scattering measurements of Chen et al. [npj Quantum Mater. 9, 40 (2024)] on FePSe 3 . These calculations faithfully explain the dynamical structure factor's momentum and energy dependence and point to a classical origin for the excitations observed in neutron spectroscopy and that the order-disorder transition can be understood in terms of thermal fluctuations overcoming the anisotropy energy.

Landau-Lifschitz-Gilbert equation↗

NASA NTRS1996

On the Use of Kronecker Operators for the Solution of Generalized Stochastic Petri Nets

We discuss how to describe the Markov chain underlying a generalized stochastic Petri net using Kronecker operators on smaller matrices. We extend previous approaches by allowing both an extensive type of marking-dependent behavior for the transitions and the presence of immediate synchronizations. The derivation of the results is thoroughly formalized, including the use of Kronecker operators in the treatment of the vanishing markings and the computation of impulse-based reward measures. We use our techniques to analyze a model whose solution using conventional methods would fail because of the state-space explosion. In the conclusion, we point out ideas to parallelize our approach.

Ciardo, Gianfranco↗

NASA NTRS2016

Hybrid Differential Dynamic Programming with Stochastic Search

Differential dynamic programming (DDP) has been demonstrated as a viable approach to low-thrust trajectory optimization, namely with the recent success of NASAs Dawn mission. The Dawn trajectory was designed with the DDP-based Static Dynamic Optimal Control algorithm used in the Mystic software. Another recently developed method, Hybrid Differential Dynamic Programming (HDDP) is a variant of the standard DDP formulation that leverages both first-order and second-order state transition matrices in addition to nonlinear programming (NLP) techniques. Areas of improvement over standard DDP include constraint handling, convergence properties, continuous dynamics, and multi-phase capability. DDP is a gradient based method and will converge to a solution nearby an initial guess. In this study, monotonic basin hopping (MBH) is employed as a stochastic search method to overcome this limitation, by augmenting the HDDP algorithm for a wider search of the solution space.

Aziz, Jonathan↗

DOE OSTI2025

Gravitational waves from supercooled phase transitions in conformal Majoron models of neutrino mass

We study supercooled first-order phase transitions above the QCD scale in a wide class of conformal Majoron-like U(1)′ models that explain the totality of active neutrino oscillation data and produce a detectable stochastic gravitational wave background (SGWB) at LIGO, LISA and ET. We place constraints on the U(1)′ breaking scale and gauge coupling using current LIGO-Virgo-Kagra data. We find that strong supercooling can be ruled out in large regions of parameter space if a SGWB is not detected by these experiments. A null signal at LIGO and ET will disfavor a type-I seesaw scale above 10 14 GeV, while a positive signal is a signature of heavy right-handed neutrinos. On the other hand, LISA will be sensitive to seesaw scales as low as a TeV, and could detect a SGWB even if the right-handed neutrinos are decoupled.

early universe particle physics↗

NASA NTRS2016

Hybrid Differential Dynamic Programming with Stochastic Search

Differential dynamic programming (DDP) has been demonstrated as a viable approach to low-thrust trajectory optimization, namely with the recent success of NASA's Dawn mission. The Dawn trajectory was designed with the DDP-based Static/Dynamic Optimal Control algorithm used in the Mystic software.1 Another recently developed method, Hybrid Differential Dynamic Programming (HDDP),2, 3 is a variant of the standard DDP formulation that leverages both first-order and second-order state transition matrices in addition to nonlinear programming (NLP) techniques. Areas of improvement over standard DDP include constraint handling, convergence properties, continuous dynamics, and multi-phase capability. DDP is a gradient based method and will converge to a solution nearby an initial guess. In this study, monotonic basin hopping (MBH) is employed as a stochastic search method to overcome this limitation, by augmenting the HDDP algorithm for a wider search of the solution space.

Aziz, Jonathan↗

DOE OSTI2022

A phase transition for finding needles in nonlinear haystacks with LASSO artificial neural networks

To fit sparse linear associations, a LASSO sparsity inducing penalty with a single hyperparameter provably allows to recover the important features (needles) with high probability in certain regimes even if the sample size is smaller than the dimension of the input vector (haystack). More recently learners known as artificial neural networks (ANN) have shown great successes in many machine learning tasks, in particular fitting nonlinear associations. Small learning rate, stochastic gradient descent algorithm and large training set help to cope with the explosion in the number of parameters present in deep neural networks. Yet few ANN learners have been developed and studied to find needles in nonlinear haystacks. Driven by a single hyperparameter, our ANN learner, like for sparse linear associations, exhibits a phase transition in the probability of retrieving the needles, which we do not observe with other ANN learners. To select our penalty parameter, we generalize the universal threshold of Donoho and Johnstone (Biometrika 81(3):425–455, 1994) which is a better rule than the conservative (too many false detections) and expensive cross-validation. In the spirit of simulated annealing, we propose a warm-start sparsity inducing algorithm to solve the high-dimensional, non-convex and non-differentiable optimization problem. We perform simulated and real data Monte Carlo experiments to quantify the effectiveness of our approach.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Theory of oblique-field magnetoresistance from spin centers in three-terminal spintronic devices

Here, we present a general stochastic Liouville theory of electrical transport across a barrier between two conductors that occurs via sequential hopping through a single defect's spin-0 to spin-1/2 transition. We find magnetoconductances similar to Hanle features (pseudo Hanle features) that originate from Pauli blocking without spin accumulation, and also predict that evolution of the defect's spin modifies the conventional Hanle response, producing an inverted Hanle signal from spin center evolution. We propose studies in oblique magnetic fields that would unambiguously determine if a magnetoconductance results from spin-center assisted transport.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Noise-induced stabilization of dynamical states with broken time-reversal symmetry

Under a high frequency drive, Josephson junctions demonstrate Shapiro steps of quantized voltage. These are dynamically stabilized states in which the phase across the junction locks to the external drive. We explore the stochastic switching between two symmetric steps at $\frac{hw}{2e}$ and –$\frac{hw}{2e}$. Surprisingly, the switching rate exhibits a pronounced nonmonotonicity as a function of temperature, violating the general expectation that transitions should become faster with temperature. As a result, we explain this behavior by realizing that the system retains memory of the dynamic state from which it is switching, thereby breaking the conventional simplifying assumptions about separations of timescales.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Flame acceleration and transition to detonation in a pre-/main-chamber combustion system

Numerical simulations are performed to study the mechanism of deflagration to detonation transition (DDT) in a pre-/main-chamber combustion system with a stoichiometric ethylene–oxygen mixture. A Godunov algorithm, fifth-order in space, and third-order in time, is used to solve the fully compressible Navier–Stokes equations on a dynamically adapting mesh. A single-step, calibrated chemical diffusive model described by Arrhenius kinetics is used for energy release and conservation between the fuel and the product. The two-dimensional simulation shows that a laminar flame grows in the pre-chamber and then develops into a jet flame as it passes through the orifice. A strong shock forms immediately ahead of the flame, reflecting off the walls and interacting with the flame front. The shock–flame interactions are crucial for the development of flame instabilities, which trigger the subsequent flame development. The DDT arises due to a shock-focusing mechanism, where multiple shocks collide at the flame front. A chemical explosive mode analysis (CEMA) criterion is developed to study the DDT ignition mode. Preliminary one-dimensional computations for a laminar propagating flame, a fast flame deflagration, and a Chapman–Jouguet detonation are conducted to demonstrate the validity of CEMA on the chemical-diffusive model, as well as to determine the proper conditioning value for CEMA diagnostic. The two-dimensional analysis with CEMA indicates that the DDT initiated by the shock-focusing mechanism can form a strong thermal expansion region at the flame front that features large positive eigenvalues for the chemical explosive mode and dominance of the local autoignition mode. Thus, the CEMA criterion proposed in this study provides a robust diagnostic for identifying autoignition-supported DDT, of which the emergence of excessive local autoignition mode is found to be a precursor. The effect of grid size, initial temperature, and orifice size are then evaluated, and results show that although the close-chamber DDT is highly stochastic, the detonation initiation mechanism remains robust.

42 ENGINEERING↗

DOE OSTI2023

Stochastic Price Generation for Evaluating Wholesale Electricity Market Bidding Strategies

This work presents a novel method for generating electricity price scenarios from statistical properties of past electricity prices using a hybrid statistical and reduced-form stochastic model. Previous work in applying stochastic differential equations (SDE) to model electricity prices has focused on daily average prices. To extend stochastic price generation methods to hourly or sub-hourly pricing, we address several weaknesses in the state-of-the-art: (1) we replace the mean-reversion component of the SDE with an ARIMA process that is better able to characterize the daily and weekly trends; (2) we extend the price-spike, or jump process to account for conditional probabilities of price spikes occurring in consecutive time steps by replacing the traditional Poisson process for modeling jumps with a generalized point process model inspired by brain neuron models; and (3) we replace the traditional method of estimating spike intensity with empirical variance with a Markov process based on observed price spike intensity transitions. The method is demonstrated with electricity prices from the US ERCOT market and a use-case example is provided for bidding an energy storage unit into the day-ahead and real-time energy markets of ERCOT using stochastic optimization methods. Results show that the the synthetic price model out performs a (naive) persistence forecast model by resulting in 24% to 47% more in profits over 168 simulated days.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

DOE OSTI2021

Resonant X-ray emission spectroscopy from broadband stochastic pulses at an X-ray free electron laser

Abstract Hard X-ray spectroscopy is an element specific probe of electronic state, but signals are weak and require intense light to study low concentration samples. Free electron laser facilities offer the highest intensity X-rays of any available light source. The light produced at such facilities is stochastic, with spikey, broadband spectra that change drastically from shot to shot. Here, using aqueous ferrocyanide, we show that the resonant X-ray emission (RXES) spectrum can be inferred by correlating for each shot the fluorescence intensity from the sample with spectra of the fluctuating, self-amplified spontaneous emission (SASE) source. We obtain resolved narrow and chemically rich information in core-to-valence transitions of the pre-edge region at the Fe K-edge. Our approach avoids monochromatization, provides higher photon flux to the sample, and allows non-resonant signals like elastic scattering to be simultaneously recorded. The spectra obtained match well with spectra measured using a monochromator. We also show that inaccurate measurements of the stochastic light spectra reduce the measurement efficiency of our approach.

Fuller, Franklin D. (ORCID:0000000237737087)↗

NASA NTRS1992

Preliminary design of a meteoroid/orbital debris shield system for a Mars mission spacecraft

A preliminary design of a spacecraft shield system to defeat meteoroids and orbital debris during a Mars mission is presented. The mission scenario is first defined in terms of stage times which include LEO, transit, low-Mars orbit, and Mars surface periods. The environment definitions for earth-orbital space debris, planetary meteoroids, and interplanetary meteoroids are next introduced. Shield system design approaches incorporate stochastic simulation, hydrocode analyses, hypervelocity impact testing, and optimization techniques. Structural design trades presented include spacecraft configuration, mission schedule, penetration risk, and total standoff distance between the bumper and wall.

Robinson, J. H.↗

DOE OSTI2021

A Kinetic Monte Carlo Approach for Simulating Cascading Transmission Line Failure

In this work, cascading transmission line failures are studied through a dynamical model of the power system operating under fixed conditions. The power grid is modeled as a stochastic dynamical system where first-principles electromechanical dynamics are excited by small Gaussian disturbances in demand and generation around a specified operating point. In this context, a single line failure is interpreted in a large deviation context as a first escape event across a surface in phase space defined by line security constraints. The resulting system of stochastic differential equations admits a transverse decomposition of the drift, which leads to considerable simplification in evaluating the quasipotential (rate function) and, consequently, computation of exit rates. Tractable expressions for the rate of transmission line failure in a restricted network are derived from large deviation theory arguments and validated against numerical simulations. Extensions to realistic settings are considered, and individual line failure models are aggregated into a Markov model of cascading failure inspired by chemical kinetics. Cascades are generated by traversing a graph composed of weighted edges representing transitions to degraded network topologies. Numerical results indicate that the Markov model can produce cascades with qualitative power-law properties similar to those observed in empirical cascades.

Kinetic Monte Carlo, rare events, Cascading Failur↗

DOE OSTI2024

Stochastic journeys of cell progenies through compartments and the role of self-renewal, symmetric and asymmetric division

Abstract Division and differentiation events by which cell populations with specific functions are generated often take place as part of a developmental programme, which can be represented by a sequence of compartments. A compartment is the set of cells with common characteristics; sharing, for instance, a spatial location or a phenotype. Differentiation events are transitions from one compartment to the next. Cells may also die or divide. We consider three different types of division events: (i) where both daughter cells inherit the mother’s phenotype (self-renewal), (ii) where only one of the daughters changes phenotype (asymmetric division), and (iii) where both daughters change phenotype (symmetric division). The self-renewal probability in each compartment determines whether the progeny of a single cell, moving through the sequence of compartments, is finite or grows without bound. We analyse the progeny stochastic dynamics with probability generating functions. In the case of self-renewal, by following one of the daughters after any division event, we may construct lifelines containing only one cell at any time. We analyse the number of divisions along such lines, and the compartment where lines terminate with a death event. Analysis and numerical simulations are applied to a five-compartment model of the gradual differentiation of hematopoietic stem cells and to a model of thymocyte development: from pre-double positive to single positive (SP) cells with a bifurcation to either SP4 or SP8 in the last compartment of the sequence.

Science & Technology - Other Topics↗

NASA NTRS1994

Multifrequency emission from hot ion disks

The discovery of a large number of gamma-emitting active galactic nuclei (AGNs) by the EGRET instrument on the Compton Gamma Ray Observatory (CGRO) has spawned a lot of theoretical interest in the high-energy and multifrequency emission from these objects. Since most of them show evidence for relativistic outflow, jet models have received most of the attention so far. However, the presence of soft photons at the center of the active nucleus and the resulting Compton drag make it difficult to produce the observed amount of MeV/GeV emission. We explore hot, two-temperature accretion disks around Kerr black holes as an alternative to relativistic beam models for the production of the high-enerty emission. The decay of neutral pions created in the hot region produces photons with energies up to several hundred MeV. Relativistic pairs created as a result of charged pion decays produce additional inverse-Compton radiation in the range of approx. 1 keV-4 MeV if the pairs are exposed to UV radiation, or in the range of approx. 40 keV-150 MeV if the pairs are exposed to soft X-rays. This suggests that high-energy flares in AGNs may be triggered by changes in the disk structure (such as phase transitions or the development of electron scattering coronae) that temporarily shield the hot inner region from UV photons emitted at larger radii, thereby reducing the optical depth for MeV/GeV gamma-rays. Stochastic processes may also play a role in accelerating the utrarelativistic electrons responsible for producing the highest energy (GeV) emission.

Maisack, Michael↗