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Partially completed extensions for stochastic programming to the AMPL/solver interface library (ASL).modeling and experimenting with stochastic recourse problems. This software is not primarily for military applications.
SSRS (Stochastic Soaring Raptor Simulator) is a generalizable, probabilistic, and predictive tool for wind energy developers, ecologists, wildlife managers and industry consultants to estimate the potential for soaring raptors to interact with operating wind turbines, without the need for site-specific data collection. Rapid expansion of wind energy development across the world has exposed the risk of turbine collisions for birds and bats. The risk to obligate soaring raptors such as golden eagles is of particular concern due to their small population and influence on ecological balance. Golden eagles rely heavily on updrafts to subsidize their flight, putting them in direct conflict with operational wind turbines that utilize the same wind resource. Understanding the behavior of soaring raptors with varying atmospheric conditions is crucial for predicting and mitigating the risk of turbine collision. This software contains a predictive movement model that simulates individual flight paths of golden eagles during updraft-subsidized long-distance flight, including migration. For a given set of atmospheric conditions, the model simulates thousands of eagles at turbine-scale spatial resolution (50m) to produce a relative presence density map. The simulated eagles rely on updrafts to pursue uninterrupted directional flight with minimal energy expenditure, following fluid-flow principles. The simulator includes a stochastic model of eagle behavior and a systematic method of accounting for spatiotemporal variations in atmospheric conditions. This framework only requires publicly available atmospheric data to estimate orographic and thermal updrafts, ensuring general usability.
Abstract This study presents a modeling approach for examining how changes in climate affect streamflow in mesoscale mountain basins dominated by snowmelt runoff. A conceptual snowmelt-runoff model was developed that is forced by daily time series of temperature and precipitation. The model can be run using either observed climate data or artificial climate data generated from a GCM or a stochastic model. The model was applied to a case-study basin, the north fork of the Clearwater River in Idaho, using stochastically generated climate scenarios. Climate scenarios were generated using a contemporaneous auto-regressive integrated moving average (CARIMA) model for temperature and a precipitation model based on a two-state first-order Markov process. A baseline climate scenario was developed that represents recently observed temperature and precipitation conditions and then 15 additional climate scenarios that represent shifts in recent conditions. For each scenario, model application produced an ensemble of 50 streamflow traces each spanning 30 yr. Results show that an increase in temperature among scenarios leads to a decrease in streamflow and vice versa. Decreases in temperature shift the basin runoff to fully snowmelt dominated, whereas increases in temperature increase the frequency of midwinter runoff events. Increasing precipitation leads to increased runoff in cases where the temperature remains the same as the observed record, but not in cases where the temperature increases. The modeling approach presented here can be used by water managers to examine which types of climate change could require modifications in water planning and operations.
Abstract Subgrid-scale (SGS) velocity variations result in gridscale sea surface flux enhancements that must be parameterized in weather and climate models. Traditional parameterizations are deterministic in that they assign a unique value of the SGS velocity flux enhancement to any given configuration of the resolved state. In this study, we assess the statistics of SGS velocity flux enhancement over a range of averaging scales (as a proxy for varying model resolution) through systematic coarse-graining of a convection-permitting atmospheric model simulation over the Indian Ocean and west Pacific warm pool. Conditioning the statistics of the SGS velocity flux enhancement on 1) the fluxes associated with the resolved winds and 2) the precipitation rate, we find that the lack of a separation between “resolved” and “unresolved” scales results in a distribution of flux enhancements for each configuration of the resolved state. That is, the SGS velocity flux enhancement should be represented stochastically rather than deterministically. The spatial and temporal statistics of the SGS velocity flux enhancement are investigated by using basic descriptive statistics and through a fit to an anisotropic space–time covariance structure. Potential spatial inhomogeneities of the statistics of the SGS velocity flux enhancement are investigated through regional analysis, although because of the relatively short duration of the simulation (9 days) distinguishing true inhomogeneity from sampling variability is difficult. Perspectives for the implementation of such a stochastic parameterization in weather and climate models are discussed.
The sequence of a promoter within a genome does not uniquely determine gene expression levels and their variability; rather, promoter sequence can additionally interact with its location in the genome, or genomic context, to shape eukaryotic gene expression. Retroviruses, such as human immunodeficiency virus-1 (HIV), integrate their genomes into those of their host and thereby provide a biomedically-relevant model system to quantitatively explore the relationship between promoter sequence, genomic context, and noise-driven variability on viral gene expression. Using an in vitro model of the HIV Tat-mediated positive-feedback loop, we previously demonstrated that fluctuations in viral Tattransactivating protein levels generate integration-site-dependent, stochastically-driven phenotypes, in which infected cells randomly ‘switch’ between high and low expressing states in a manner that may be related to viral latency. Here we extended this model and designed a forward genetic screen to systematically identify genetic elements in the HIV LTR promoter that modulate the fraction of genomic integrations that specify ‘Switching’ phenotypes. Our screen identified mutations in core promoter regions, including Sp1 and TATA transcription factor binding sites, which increased the Switching fraction several fold. By integrating single-cell experiments with computational modeling, we further investigated the mechanism of Switching-fraction enhancement for a selected Sp1 mutation. Our experimental observations demonstrated that the Sp1 mutation both impaired Tat-transactivated expression and also altered basal expression in the absence of Tat. Computational analysis demonstrated that the observed change in basal expression could contribute significantly to the observed increase in viral integrations that specify a Switching phenotype, provided that the selected mutation affected Tat-mediated noise amplification differentially across genomic contexts. Our study thus demonstrates a methodology to identify and characterize promoter elements that affect the distribution of stochastic phenotypes over genomic contexts, and advances our understanding of how promoter mutations may control the frequency of latent HIV infection.
We present StochSS: Stochastic Simulation as a Service, an integrated development environment for modeling and simulation of both deterministic and discrete stochastic biochemical systems in up to three dimensions. An easy to use graphical user interface enables researchers to quickly develop and simulate a biological model on a desktop or laptop, which can then be expanded to incorporate increasing levels of complexity. StochSS features state-of-the-art simulation engines. As the demand for computational power increases, StochSS can seamlessly scale computing resources in the cloud. In addition, StochSS can be deployed as a multi-user software environment where collaborators share computational resources and exchange models via a public model repository. We also demonstrate the capabilities and ease of use of StochSS with an example of model development and simulation at increasing levels of complexity.
Radiation exposure of the hematopoietic system that results in a radiation dose to bone marrow of more than 100 mGy leads to an increase in the risk of leukemia in humans. Excess relative risk of leukemia was observed in cohorts whose members lived in the territories of the Southern Urals that were radioactively contaminated in the 1950s. As part of the dosimetric support of epidemiological studies of these cohorts, an original methodology for stochastic bone dosimetric modeling was developed, termed the Stochastic Parametric Skeletal Dosimetry (SPSD) model. The purpose of this work was to present the anatomical and morphological bases of the SPSD model, which includes an assessment of the parameters of the microstructure of the trabecular bone in the hematopoietic areas of the human skeleton, as well as a description of the macrostructural division (segmentation) of hematopoietic areas into simple bone segments. As a result, an anatomical-morphological basis of the SPSD model was created based on published data. Data collection work included the analysis of original articles, atlases, manuals, monographs and the formation of primary data files. Data on the duration of hematopoiesis in various parts of the skeleton; and data on age-related changes in the microstructure and linear dimensions of human bones and their segments were analyzed. The paper describes the full set of parameters to be used for the dosimetric model for newborns, children aged 1, 5 and 10 years, as well as for adolescents aged 15 years and adults; for the latter, sex differences in bone size were considered. In total, the SPSD model includes 289 unique basic (bone) phantom segments, each of which is described by 7 or more parameters describing the microstructure, thickness of the cortical layer and linear dimensions. Population variability was estimated for each parameter. The approach to SPSD modeling, i.e., the use of simple geometric shapes, was successfully verified using independent datasets on bone masses and volumes.
Optical Stochastic Cooling (OSC) has been considered for future high-luminosity colliders as it offers much faster cooling time in comparison to the micro-wave stochastic cooling. The OSC technique relies on collecting and amplifying a broadband optical signal from a pickup undulator and feeding the amplified signal back to the beam. It creates a corrective kick in a kicker undulator. Owing to its superb gain qualities and broadband amplification features, Titanium:Sapphire medium has been considered as a gain medium for the optical amplifier (OA) needed in the OSC*. A limiting factor for any OA used in OSC is the possibility of nonlinear phase distortions. In this paper we experimentally measure phase distortions by inserting a single-pass OA into one leg of a Mach-Zehnder interferometer. The measurement results are used to estimate the reduction of the corrective kick a particle would receive due to these phase distortions in the kicker undulator.
Optical Stochastic Cooling (OSC), a beam cooling technique based on Stochastic Cooling, is in the early stages of experimental development. It uses radiation produced by the beam in an undulator magnet (the pickup) to correct the momentum deviation of particles downstream in another undulator (the kicker). The OSC mechanism was recently demonstrated at Fermilab’s IOTA ring using a passive configuration. However, the cooling rate of OSC can be dramatically increased by first amplifying the undulator radiation before applying the corrective kick. In collaboration with the IOTA experiment, we developed a computational model of the OSC mechanism. This paper presents beam-dynamics simulations of the amplified-OSC configuration. We implement a model of intrabeam scattering and study the effects on beam equilibrium and diffusion rate as a function of bunch charge. Finally, we investigate the phase-space dynamics with various coupling configurations between the transverse and longitudinal planes.
Short toroidal Alfven eigenmode (TAE) avalanche bursts in the National Spherical Torus Experiment (NSTX) cause a drop in the neutron rate and sometimes a loss of neutral beam ions at or near the full injection energy over an extended range of pitch angles. The simultaneous loss of wide ranges of pitch angle suggests stochastic transport of the beam ions occurs. When beam ion orbits are followed with a guiding center code that incorporates plasma's magnetic equilibrium plus the measured modes, the predicted ranges of lost pitch angle are similar to those seen in the experiment, with distinct populations of trapped and passing orbits lost. These correspond to domains where the stochasticity extends in the orbit phase space from the region of beam ion deposition to the loss boundary.
The focus of the project is the development of mathematical methods and high-performance com- putational tools for stochastic simulations, with a particular emphasis on computations on extreme scales. The core of the project revolves around the design of highly e cient and scalable numer- ical algorithms that can adaptively and accurately, in high dimensional spaces, resolve stochastic problems with limited smoothness, even containing discontinuities.
The focus of the project is the development of mathematical methods and high-performance computational tools for stochastic simulations, with a particular emphasis on computations on extreme scales. The core of the project revolves around the design of highly efficient and scalable numerical algorithms that can adaptively and accurately, in high dimensional spaces, resolve stochastic problems with limited smoothness, even containing discontinuities.
Acoustic full waveform algorithms, such as Paracousti, provide deterministic solutions in complex, 3-D variable environments. In reality, environmental and source characteristics are often only known in a statistical sense. Thus, to fully characterize the expected sound levels within an environment, this uncertainty in environmental and source factors should be incorporated into the acoustic simulations. Performing Monte Carlo (MC) simulations is one method of assessing this uncertainty, but it can quickly become computationally intractable for realistic problems. An alternative method, using the technique of stochastic partial differential equations (SPDE), allows computation of the statistical properties of output signals at a fraction of the computational cost of MC. Paracousti-UQ solves the SPDE system of 3-D acoustic wave propagation equations and provides estimates of the uncertainty of the output simulated wave field (e.g., amplitudes, waveforms) based on estimated probability distributions of the input medium and source parameters. This report describes the derivation of the stochastic partial differential equations, their implementation, and comparison of Paracousti-UQ results with MC simulations using simple models.
Performing stochastic inversion on a computationally expensive forward simulation model with a high-dimensional uncertain parameter space (e.g. a spatial random field) is computationally prohibitive even when gradient information can be computed efficiently. Moreover, the ‘nonlinear’ mapping from parameters to observables generally gives rise to non-Gaussian posteriors even with Gaussian priors, thus hampering the use of efficient inversion algorithms designed for models with Gaussian assumptions. In this paper, we propose a novel Bayesian stochastic inversion methodology, which is characterized by a tight coupling between the gradient-based Langevin Markov Chain Monte Carlo (LMCMC) method and a kernel principal component analysis (KPCA). This approach addresses the ‘curse-of-dimensionality’ via KPCA to identify a low-dimensional feature space within the high-dimensional and nonlinearly correlated parameter space. In addition, non-Gaussian posterior distributions are estimated via an efficient LMCMC method on the projected low-dimensional feature space. We will demonstrate this computational framework by integrating and adapting our recent data-driven statistics-on-manifolds constructions and reduction-through-projection techniques to a linear elasticity model.
In many material systems, man-made or natural, we have an incomplete knowledge of geometric or material properties, which leads to uncertainty in predicting their performance under dynamic loading. Given the uncertainty and a high degree of spatial variability in properties of materials subjected to impact, a stochastic theory of continuum mechanics would be useful for modeling dynamic response of such systems. Peridynamic theory is such a theory. It is formulated as an integro- differential equation that does not employ spatial derivatives, and provides for a consistent formulation of both deformation and failure of materials. We discuss an approach to stochastic peridynamic theory and illustrate the formulation with examples of impact loading of geological materials with uncorrelated or correlated material properties. We examine wave propagation and damage to the material. The most salient feature is the absence of spallation, referred to as disorder toughness, which generalizes similar results from earlier quasi-static damage mechanics. Acknowledgements This research was made possible by the support from DTRA grant HDTRA1-08-10-BRCWM. I thank Dr. Martin Ostoja-Starzewski for introducing me to the mechanics of random materials and collaborating with me throughout and after this DTRA project.
Performing stochastic inversion on a computationally expensive forward simulation model with a high-dimensional uncertain parameter space (e.g. a spatial random field) is computationally prohibitive even with gradient information provided. Moreover, the ‘nonlinear’ mapping from parameters to observables generally gives rise to non-Gaussian posteriors even with Gaussian priors, thus hampering the use of efficient inversion algorithms designed for models with Gaussian assumptions. In this work, we propose a novel Bayesian stochastic inversion methodology, characterized by a tight coupling between a gradient-based Langevin Markov Chain Monte Carlo (LMCMC) method and a kernel principal component analysis (KPCA). This approach addresses the ‘curse-of-dimensionality’ via KPCA to identify a low-dimensional feature space within the high-dimensional and nonlinearly correlated spatial random field. Moreover, non-Gaussian full posterior probability distribution functions are estimated via an efficient LMCMC method on both the projected low-dimensional feature space and the recovered high-dimensional parameter space. We demonstrate this computational framework by integrating and adapting recent developments such as data-driven statistics-on-manifolds constructions and reduction-through-projection techniques to solve inverse problems in linear elasticity.
Nonlinear integrable optics, the basis of IOTA, is a very special form of Hamiltonian system, called completely integrable. The consequences are many, most importantly the absence of fixed points that are in one-to-one correspondence with (overlapping) resonances. This, in turn, does not limit the dynamic aperture and allows large amplitude dependent tune shifts without adverse effects. In fact, it helps significantly in alleviating issues with collective instabilities. We developed and tested different numerical methods to give a more complete picture of the dynamics of integrable and near-integrable nonlinear Hamiltonian systems consisting of motion of charged particles in electromagnetic fields. Comparison of the results allowed us to discern real phenomena from numerical artifacts and come up with conclusions that will facilitate pushing the intensity frontier in beam dynamics even further for the benefit of the accelerator community as a whole and society as the consequence of the science and technological advancements it will make possible. We concluded that, while novel structure preserving integrators would be ideal, symplectic methods under mild restrictions offer adequate invariant preservation. We especially highlighted the very good performance of the Stormer-Verlet method at low accuracy and a modified Lobatto method at high accuracy for the Integrable Optics Test Accelerator (IOTA). However, we showed that symplectic integrators are limited by numerically induced resonances, which make interpretation of some simulation results challenging. These limitations and workarounds have been addressed.The nonlinear integrable optics test accelerator IOTA at Fermilab -- a very special experimental accelerator designed to investigate nonlinear optics under severe space-charge conditions – has recently completed its construction and initial commissioning of the ring has begun. We report first, under 2 (a) below: the progress on the nonlinear tune-shift measurements for various values of the nonlinear strength potential and their comparison with theoretical expectations, thus benchmarking the nonlinear characteristics of the ring; then, under 2 (b) below: the progress on simulation and design of a gas-jet monitor to measure beam profile and in particular its diffusive halo, expected to develop during stochastic diffusion of large amplitude particles under nonlinear forces of the magnetic lattice and Coulomb space-charge. Since the development of a proton beam source in IOTA is delayed and to be completed only in the future pending financial support, the gas-jet monitor is planned for testing with real proton beams elsewhere at Fermilab (e.g. in the Main Injector or PIP-II source possibly). Once proton beams are available in IOTA, the understanding of the nonlinear properties of IOTA combined with the developed gas-jet monitor, will enable a thorough experimental analysis of nonlinear stochastic diffusion in IOTA nonlinear ring, and boosted by proper theoretical understanding of the same.
Deforming objects in the world of the small has proven a much more complex task than just bending a common-sized object like a spoon. Over the last decade, it has become clear that the application of stress on micron-sized objects, such as micropillars, leads to abrupt and stochastic plastic strain jumps that do not satisfy Weibull statistics (as expected for uncorrelated defect yielding) but instead seem to follow highly wide, power-law distributions, pointing towards cooperative dislocation plasticity. Are power-law distributed plastic events the rule or the exception in crystals? If the rule, can we design protocols to control and suppress them in order to achieve deterministic and smooth microforming processes? We propose to combine experiments and theory to unravel the mysteries of abrupt microplastic deformation in a natural dislocation environment: micron-sized grains (\micrograins") of polycrystals. We propose a novel experimental design that utilizes nanoindentation and 4-point bending techniques on the substrate of polycrystalline thin films of two typical FCC metals (Al and Cu), and make concrete theoretical conjectures, based on intuition built from previous theoretical and experimental efforts in micropillar compression and nanoindentation. Based on a wide set of observations over the last decade, we put forward two distinct hypotheses that we propose to investigate in both theory and experiments: Our first conjecture is that crystal plasticity in the central region of micron-sized grains has micropillar-like stochastic features: power-law plastic strain jumps at stresses above the macroscale yield strength, displaying strong size and rate effects. We will demonstrate this similarity in spherical nanoindentation experiments in the central-region of multi-orientation grains of Al and Cu thin films. Al and Cu are selected for their disparity in stacking fault energy and consequently, their different propensity for cross-slip relaxation; however, our protocol may be applied to any crystalline material of technological interest. We will test our hypothesis by performing two-dimensional extended discrete dislocation plasticity (2.5D-DDP) simulations, inspired by comparable successful studies of micropillar plasticity, and extended to model nanoindentation with two slip systems and on a surface of a bicrystal with microhard grain-boundaries (GB), ie. not allowing dislocation absorption (116). Our model will include effective three dimensional dislocation mechanisms such as dislocation multiplication and double-cross-slip assisted glide. Second, we hypothesize that the application of uniform in-plane stress on our thin films below the yield point can smoothen the micrograin plastic response during nanoindentation. On a technological level, we propose that indentation-induced localization (sink-in) may be diminished by the application of concurrent in-plane stress that activates slow, viscoplastic relaxations near GBs. We aim to demonstrate our hypothesis through a 4-point bending apparatus that introduces a homogeneous in-plane stress state before indentation. We will perform simulations of a coarse-grained mesoscale theory of plasticity in a system with microhard GBs, benchmarked through 2.5D-DDP simulations, which will capture the effects of slow viscoplastic relaxations. Our nanoindentation abrupt event statistics studies, either in the micrograin interior or near GBs, will be correlated to direct observations of induced surface dislocation microstructures. For we will use TEM-based methods (PACOM/TKD) in combination with EBSD. Indents placed in the center of grains will be analyzed based on the orientation of the grain, while those near to GBs will be analyzed based on the orientation of each grain, the distance from the GB and the 5 degrees of freedom of the GB.