Stochastic compartmental analysis - Model and least squares estimation from time series data
Biomathematical model and least square estimation from time series data of discrete particle population in stochastic compartmental system
Hartley, H. O.↗
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A stochastic differential equation model of diurnal cortisol patterns
Circadian modulation of episodic bursts is recognized as the normal physiological pattern of diurnal variation in plasma cortisol levels. The primary physiological factors underlying these diurnal patterns are the ultradian timing of secretory events, circadian modulation of the amplitude of secretory events, infusion of the hormone from the adrenal gland into the plasma, and clearance of the hormone from the plasma by the liver. Each measured plasma cortisol level has an error arising from the cortisol immunoassay. We demonstrate that all of these three physiological principles can be succinctly summarized in a single stochastic differential equation plus measurement error model and show that physiologically consistent ranges of the model parameters can be determined from published reports. We summarize the model parameters in terms of the multivariate Gaussian probability density and establish the plausibility of the model with a series of simulation studies. Our framework makes possible a sensitivity analysis in which all model parameters are allowed to vary simultaneously. The model offers an approach for simultaneously representing cortisol's ultradian, circadian, and kinetic properties. Our modeling paradigm provides a framework for simulation studies and data analysis that should be readily adaptable to the analysis of other endocrine hormone systems.
NASA Discipline Space Human Factors↗
Multi-Parent Clustering Algorithms from Stochastic Grammar Data Models
We introduce a statistical data model and an associated optimization-based clustering algorithm which allows data vectors to belong to zero, one or several parent clusters.
Clustering↗
Modular and Stochastic Approaches to Molecular Pathway Models of ATM, TGF beta, and WNT Signaling
Deterministic pathway models that describe the biochemical interactions of a group of related proteins, their complexes, activation through kinase, etc. are often the basis for many systems biology models. Low dose radiation effects present a unique set of challenges to these models including the importance of stochastic effects due to the nature of radiation tracks and small number of molecules activated, and the search for infrequent events that contribute to cancer risks. We have been studying models of the ATM, TGF -Smad and WNT signaling pathways with the goal of applying pathway models to the investigation of low dose radiation cancer risks. Modeling challenges include introduction of stochastic models of radiation tracks, their relationships to more than one substrate species that perturb pathways, and the identification of a representative set of enzymes that act on the dominant substrates. Because several pathways are activated concurrently by radiation the development of modular pathway approach is of interest.
Cucinotta, Francis A.↗
US Tropical Cyclone Activity in the 2030s Based on Projected Changes in Tropical Sea-Surface Temperature
We use a statistical tropical cyclone (TC) model, the North Atlantic Stochastic Hurricane Model (NASHM), in combination with sea-surface temperature (SST) projections from climate models, to estimate regional changes in US TC activity into the 2030s. NASHM is trained on historical variations in TC characteristics with two SST indices: global-tropical mean SST and the difference between tropical North-Atlantic (NA) SST and the rest of the global tropics, often referred to as “relative SST.” Testing confirms the model’s ability to reproduce historical US TC activity, as well as to make skillful predictions. When NASHM is driven by SST projections into the 2030s, overall NA annual TC counts increase, and the fractional increase is the greatest at the highest wind intensities. However, an eastward anomaly in mean TC tracks and an eastward shift in TC formation region result in a geographically-varied signal in US coastal activity. Florida’s Gulf coast is projected to see significant increases in TC activity, compared to the long-term historical mean, and these increases are fractionally greatest at the highest intensities. By contrast, the northwestern US Gulf and the US East Coast will see little change.
tropical cyclone (TC) model↗
Using Markov Models of Fault Growth Physics and Environmental Stresses to Optimize Control Actions
A generalized Markov chain representation of fault dynamics is presented for the case that available modeling of fault growth physics and future environmental stresses can be represented by two independent stochastic process models. A contrived but representatively challenging example will be presented and analyzed, in which uncertainty in the modeling of fault growth physics is represented by a uniformly distributed dice throwing process, and a discrete random walk is used to represent uncertain modeling of future exogenous loading demands to be placed on the system. A finite horizon dynamic programming algorithm is used to solve for an optimal control policy over a finite time window for the case that stochastic models representing physics of failure and future environmental stresses are known, and the states of both stochastic processes are observable by implemented control routines. The fundamental limitations of optimization performed in the presence of uncertain modeling information are examined by comparing the outcomes obtained from simulations of an optimizing control policy with the outcomes that would be achievable if all modeling uncertainties were removed from the system.
Bole, Brian↗
Stochastic crew motion modeling.
Representative data of actual forces and moments applicable to large spacecraft attitude control system for typical crew activities obtained through simulation programs
Hendricks, T. C.↗
Multi-Parent Clustering Algorithms from Stochastic Grammar Data Models
We introduce a statistical data model and an associated optimization-based clustering algorithm which allows data vectors to belong to zero, one or several "parent" clusters. For each data vector the algorithm makes a discrete decision among these alternatives. Thus, a recursive version of this algorithm would place data clusters in a Directed Acyclic Graph rather than a tree. We test the algorithm with synthetic data generated according to the statistical data model. We also illustrate the algorithm using real data from large-scale gene expression assays.
Mjoisness, Eric↗
GUI to Facilitate Research on Biological Damage from Radiation
A graphical-user-interface (GUI) computer program has been developed to facilitate research on the damage caused by highly energetic particles and photons impinging on living organisms. The program brings together, into one computational workspace, computer codes that have been developed over the years, plus codes that will be developed during the foreseeable future, to address diverse aspects of radiation damage. These include codes that implement radiation-track models, codes for biophysical models of breakage of deoxyribonucleic acid (DNA) by radiation, pattern-recognition programs for extracting quantitative information from biological assays, and image-processing programs that aid visualization of DNA breaks. The radiation-track models are based on transport models of interactions of radiation with matter and solution of the Boltzmann transport equation by use of both theoretical and numerical models. The biophysical models of breakage of DNA by radiation include biopolymer coarse-grained and atomistic models of DNA, stochastic- process models of deposition of energy, and Markov-based probabilistic models of placement of double-strand breaks in DNA. The program is designed for use in the NT, 95, 98, 2000, ME, and XP variants of the Windows operating system.
Cucinotta, Frances A.↗
The Analysis of the Patterns of Radiation-Induced DNA Damage Foci by a Stochastic Monte Carlo Model of DNA Double Strand Breaks Induction by Heavy Ions and Image Segmentation Software
To create a generalized mechanistic model of DNA damage in human cells that will generate analytical and image data corresponding to experimentally observed DNA damage foci and will help to improve the experimental foci yields by simulating spatial foci patterns and resolving problems with quantitative image analysis. Material and Methods: The analysis of patterns of RIFs (radiation-induced foci) produced by low- and high-LET (linear energy transfer) radiation was conducted by using a Monte Carlo model that combines the heavy ion track structure with characteristics of the human genome on the level of chromosomes. The foci patterns were also simulated in the maximum projection plane for flat nuclei. Some data analysis was done with the help of image segmentation software that identifies individual classes of RIFs and colocolized RIFs, which is of importance to some experimental assays that assign DNA damage a dual phosphorescent signal. Results: The model predicts the spatial and genomic distributions of DNA DSBs (double strand breaks) and associated RIFs in a human cell nucleus for a particular dose of either low- or high-LET radiation. We used the model to do analyses for different irradiation scenarios. In the beam-parallel-to-the-disk-of-a-flattened-nucleus scenario we found that the foci appeared to be merged due to their high density, while, in the perpendicular-beam scenario, the foci appeared as one bright spot per hit. The statistics and spatial distribution of regions of densely arranged foci, termed DNA foci chains, were predicted numerically using this model. Another analysis was done to evaluate the number of ion hits per nucleus, which were visible from streaks of closely located foci. In another analysis, our image segmentaiton software determined foci yields directly from images with single-class or colocolized foci. Conclusions: We showed that DSB clustering needs to be taken into account to determine the true DNA damage foci yield, which helps to determine the DSB yield. Using the model analysis, a researcher can refine the DSB yield per nucleus per particle. We showed that purely geometric artifacts, present in the experimental images, can be analytically resolved with the model, and that the quantization of track hits and DSB yields can be provided to the experimentalists who use enumeration of radiation-induced foci in immunofluorescence experiments using proteins that detect DNA damage. An automated image segmentaiton software can prove useful in a faster and more precise object counting for colocolized foci images.
Ponomarev, Artem↗
A Multiscale Progressive Failure Modeling Methodology for Composites that Includes Fiber Strength Stochastics
A multiscale modeling methodology was developed for continuous fiber composites that incorporates a statistical distribution of fiber strengths into coupled multiscale micromechanics/finite element (FE) analyses. A modified two-parameter Weibull cumulative distribution function, which accounts for the effect of fiber length on the probability of failure, was used to characterize the statistical distribution of fiber strengths. A parametric study using the NASA Micromechanics Analysis Code with the Generalized Method of Cells (MAC/GMC) was performed to assess the effect of variable fiber strengths on local composite failure within a repeating unit cell (RUC) and subsequent global failure. The NASA code FEAMAC and the ABAQUS finite element solver were used to analyze the progressive failure of a unidirectional SCS-6/TIMETAL 21S metal matrix composite tensile dogbone specimen at 650 degC. Multiscale progressive failure analyses were performed to quantify the effect of spatially varying fiber strengths on the RUC-averaged and global stress-strain responses and failure. The ultimate composite strengths and distribution of failure locations (predominately within the gage section) reasonably matched the experimentally observed failure behavior. The predicted composite failure behavior suggests that use of macroscale models that exploit global geometric symmetries are inappropriate for cases where the actual distribution of local fiber strengths displays no such symmetries. This issue has not received much attention in the literature. Moreover, the model discretization at a specific length scale can have a profound effect on the computational costs associated with multiscale simulations.models that yield accurate yet tractable results.
Generalized Method of Cells↗
Modeling laser velocimeter signals as triply stochastic Poisson processes
Previous models of laser Doppler velocimeter (LDV) systems have not adequately described dual-scatter signals in a manner useful for analysis and simulation of low-level photon-limited signals. At low photon rates, an LDV signal at the output of a photomultiplier tube is a compound nonhomogeneous filtered Poisson process, whose intensity function is another (slower) Poisson process with the nonstationary rate and frequency parameters controlled by a random flow (slowest) process. In the present paper, generalized Poisson shot noise models are developed for low-level LDV signals. Theoretical results useful in detection error analysis and simulation are presented, along with measurements of burst amplitude statistics. Computer generated simulations illustrate the difference between Gaussian and Poisson models of low-level signals.
Mayo, W. T., Jr.↗
Ion acceleration in impulsive solar flares
Nonrelativistic spectra of protons and ions accelerated in impulsive solar flares are derived using more realistic turbulence power spectra. The calculation is based on a particle transport equation extracted from a second step acceleration model containing stochastic acceleration. The turbulence model is generalized to waves with a small angle to the magnetic field vector and to turbulence power spectra with spectral indices s smaller than 2. Due to the occurrence of impulsive flares at low coronal heights, Coulomb losses at the dense coronal plasma and diffusive particle escape are taken into account. The ion spectra show deviations from long-duration spectra near the Coulomb barrier, where the losses become maximal. The Z-squared/A-dependence of the Coulomb losses leads to spectral variations for different ions. We present a method to estimate the turbulence parameters and injection conditions of the flare particles using ion ratios like Fe/O of impulsive flares.
Steinacker, Jurgen↗
Radiation-Spray Coupling for Realistic Flow Configurations
Three Large Eddy Simulations (LES) for a lean-direct injection (LDI) combustor are performed and compared. In addition to the cold flow simulation, the effect of radiation coupling with the multi-physics reactive flow is analyzed. The flame let progress variable approach is used as a subgrid combustion model combined with a stochastic subgrid model for spray atomization and an optically thin radiation model. For accurate chemistry modeling, a detailed Jet-A surrogate mechanism is utilized. To achieve realistic inflow, a simple recycling technique is performed at the inflow section upstream of the swirler. Good comparison is shown with the experimental data mean and root mean square profiles. The effect of combustion is found to change the shape and size of the central recirculation zone. Radiation is found to change the spray dynamics and atomization by changing the heat release distribution and the local temperature values impacting the evaporation process. The simulation with radiation modeling shows wider range of droplet size distribution by altering the evaporation rate. The current study proves the importance of radiation modeling for accurate prediction in realistic spray combustion configurations, even for low pressure systems.
El-Asrag, Hossam↗
Unsupervised Detection of Planetary Craters by a Marked Point Process
With the launch of several planetary missions in the last decade, a large amount of planetary images is being acquired. Preferably, automatic and robust processing techniques need to be used for data analysis because of the huge amount of the acquired data. Here, the aim is to achieve a robust and general methodology for crater detection. A novel technique based on a marked point process is proposed. First, the contours in the image are extracted. The object boundaries are modeled as a configuration of an unknown number of random ellipses, i.e., the contour image is considered as a realization of a marked point process. Then, an energy function is defined, containing both an a priori energy and a likelihood term. The global minimum of this function is estimated by using reversible jump Monte-Carlo Markov chain dynamics and a simulated annealing scheme. The main idea behind marked point processes is to model objects within a stochastic framework: Marked point processes represent a very promising current approach in the stochastic image modeling and provide a powerful and methodologically rigorous framework to efficiently map and detect objects and structures in an image with an excellent robustness to noise. The proposed method for crater detection has several feasible applications. One such application area is image registration by matching the extracted features.
Troglio, G.↗
A coalescence/dispersion model for turbulent flame stability
A stochastic mixing model is employed that couples finite rate mixing with finite rate combustion chemistry to examine the effects of combustor inlet conditions on the ignition limits of lean premixed turbulent flames. The kinetics of the fuel-oxidation process is described by means of a two-step reaction mechanism. The model predictions of the lean ignition limits of premixed turbulent propane-air flames are verified through comparisons with data in the literature. The variations of the lean limits are found to compare favorably with experimental magnitudes and trends.
Radhakrishnan, K.↗
An extended structure-based model based on a stochastic eddy-axis evolution equation
We have proposed and implemented an extension of the structure-based model for weak deformations. It was shown that the extended model will correctly reduce to the form of standard k-e models for the case of equilibrium under weak mean strain. The realizability of the extended model is guaranteed by the method of its construction. The predictions of the proposed model were very good for rotating homogeneous shear flows and for irrotational axisymmetric contraction, but were seriously deficient in the case of plane strain and axisymmetric expansion. We have concluded that the problem behind these difficulties lies in the algebraic constitutive equation relating the Reynolds stresses to the structure parameters rather than in the slow model developed here. In its present form, this equation assumes that under irrotational strain the principal axes of the Reynolds stresses remain locked onto those of the eddy-axis tensor. This is correct in the RDT limit, but inappropriate under weaker mean strains, when the non-linear eddy-eddy interactions tend to misalign the two sets of principal axes and create some non-zero theta and gamma.
Kassinos, S. C.↗
Stochastic Feedforward Control Technique
Class of commanded trajectories modeled as stochastic process. Advanced Transport Operating Systems (ATOPS) research and development program conducted by NASA Langley Research Center aimed at developing capabilities for increases in capacities of airports, safe and accurate flight in adverse weather conditions including shear, winds, avoidance of wake vortexes, and reduced consumption of fuel. Advances in techniques for design of modern controls and increased capabilities of digital flight computers coupled with accurate guidance information from Microwave Landing System (MLS). Stochastic feedforward control technique developed within context of ATOPS program.
Halyo, Nesim↗