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At least 73 records · Page 4

Symbolic Analysis of Concurrent Programs with Polymorphism

The current trend of multi-core and multi-processor computing is causing a paradigm shift from inherently sequential to highly concurrent and parallel applications. Certain thread interleavings, data input values, or combinations of both often cause errors in the system. Systematic verification techniques such as explicit state model checking and symbolic execution are extensively used to detect errors in such systems [7, 9]. Explicit state model checking enumerates possible thread schedules and input data values of a program in order to check for errors [3, 9]. To partially mitigate the state space explosion from data input values, symbolic execution techniques substitute data input values with symbolic values [5, 7, 6]. Explicit state model checking and symbolic execution techniques used in conjunction with exhaustive search techniques such as depth-first search are unable to detect errors in medium to large-sized concurrent programs because the number of behaviors caused by data and thread non-determinism is extremely large. We present an overview of abstraction-guided symbolic execution for concurrent programs that detects errors manifested by a combination of thread schedules and data values [8]. The technique generates a set of key program locations relevant in testing the reachability of the target locations. The symbolic execution is then guided along these locations in an attempt to generate a feasible execution path to the error state. This allows the execution to focus in parts of the behavior space more likely to contain an error.

Rungta, Neha Shyam↗

Resonance line transfer with partial redistribution. IV - A generalized formulation for lines with common upper states. V - The solar Ca II lines

A generalized formulation is given for treating partial redistribution effects in transfer problems in resonance lines with common upper states. The formulation allows explicitly for the possibility that several spectral lines may arise in transitions from a given upper level to several sharp lower levels, including, for example, the ground state and metastable states. Line profiles for the Ca II H and K lines have been calculated, accounting for the partial frequency coherence of scattered photons. These profiles are compared with calculations made with identical atomic and atmospheric models but assuming complete redistribution. Very significant differences between the profiles obtained using these two different physical descriptions of the scattering process are found, and it is now apparent that the assumption of complete redistribution is a serious oversimplification of the actual physical situation. The results question the validity of equating brightness temperatures observed at K(sub 1) in stellar spectra with minimum temperatures in stellar chromospheres; it appears likely that such a procedure will systematically underestimate the value of T-min.

Milkey, R. W.↗

The equation of state for stellar envelopes. III - Thermodynamic quantities

A method is described for deriving general expressions for all thermodynamic quantities of interest of a partially ionized multicomponent gas in terms of derivatives of the free energy. Explicit analytical formulas for all derivatives required in the evaluation of these quantities are given. Representative results for a hydrogen-helium mixture are shown.

Daeppen, Werner↗

Exponential Finite-Difference Technique

Report discusses use of explicit exponential finite-difference technique to solve various diffusion-type partial differential equations. Study extends technique to transient-heat-transfer problems in one dimensional cylindrical coordinates and two and three dimensional Cartesian coordinates and to some nonlinear problems in one or two Cartesian coordinates.

Handschuh, Robert F.↗

Optimal Limited Contingency Planning

For a given problem, the optimal Markov policy over a finite horizon is a conditional plan containing a potentially large number of branches. However, there are applications where it is desirable to strictly limit the number of decision points and branches in a plan. This raises the question of how one goes about finding optimal plans containing only a limited number of branches. In this paper, we present an any-time algorithm for optimal k-contingency planning. It is the first optimal algorithm for limited contingency planning that is not an explicit enumeration of possible contingent plans. By modelling the problem as a partially observable Markov decision process, it implements the Bellman optimality principle and prunes the solution space. We present experimental results of applying this algorithm to some simple test cases.

Meuleau, Nicolas↗

The KASE approach to domain-specific software systems

Designing software systems, like all design activities, is a knowledge-intensive task. Several studies have found that the predominant cause of failures among system designers is lack of knowledge: knowledge about the application domain, knowledge about design schemes, knowledge about design processes, etc. The goal of domain-specific software design systems is to explicitly represent knowledge relevant to a class of applications and use it to partially or completely automate various aspects of the designing systems within that domain. The hope is that this would reduce the intellectual burden on the human designers and lead to more efficient software development. In this paper, we present a domain-specific system built on top of KASE, a knowledge-assisted software engineering environment being developed at the Stanford Knowledge Systems Laboratory. We introduce the main ideas underlying the construction of domain specific systems within KASE, illustrate the application of the idea in the synthesis of a system for tracking aircraft from radar signals, and discuss some of the issues in constructing domain-specific systems.

Bhansali, Sanjay↗

Test particle propagation in magnetostatic turbulence. 2: The local approximation method

An approximation method for statistical mechanics is presented and applied to a class of problems which contains a test particle propagation problem. All of the available basic equations used in statistical mechanics are cast in the form of a single equation which is integrodifferential in time and which is then used as the starting point for the construction of the local approximation method. Simplification of the integrodifferential equation is achieved through approximation to the Laplace transform of its kernel. The approximation is valid near the origin in the Laplace space and is based on the assumption of small Laplace variable. No other small parameter is necessary for the construction of this approximation method. The n'th level of approximation is constructed formally, and the first five levels of approximation are calculated explicitly. It is shown that each level of approximation is governed by an inhomogeneous partial differential equation in time with time independent operator coefficients. The order in time of these partial differential equations is found to increase as n does. At n = 0 the most local first order partial differential equation which governs the Markovian limit is regained.

Klimas, A. J.↗

Fourth order difference methods for hyperbolic IBVP's

Fourth order difference approximations of initial-boundary value problems for hyperbolic partial differential equations are considered. We use the method of lines approach with both explicit and compact implicit difference operators in space. The explicit operator satisfies an energy estimate leading to strict stability. For the implicit operator we develop boundary conditions and give a complete proof of strong stability using the Laplace transform technique. We also present numerical experiments for the linear advection equation and Burgers' equation with discontinuities in the solution or in its derivative. The first equation is used for modeling contact discontinuities in fluid dynamics, the second one for modeling shocks and rarefaction waves. The time discretization is done with a third order Runge-Kutta TVD method. For solutions with discontinuities in the solution itself we add a filter based on second order viscosity. In case of the non-linear Burger's equation we use a flux splitting technique that results in an energy estimate for certain different approximations, in which case also an entropy condition is fulfilled. In particular we shall demonstrate that the unsplit conservative form produces a non-physical shock instead of the physically correct rarefaction wave. In the numerical experiments we compare our fourth order methods with a standard second order one and with a third order TVD-method. The results show that the fourth order methods are the only ones that give good results for all the considered test problems.

Gustafsson, Bertil↗

Microphysical Modelling of Polar Stratospheric Clouds During the 1999-2000 Winter

The evolution of the 1999-2000 Arctic winter has been examined using a microphysical/photochemical model run along diabatic trajectories. A large number of trajectories have been generated, filling the vortex throughout the region of polar stratospheric cloud (PSC) formation, and extending from November until the vortex breakup, in order to provide representative sampling of the evolution of PSCs and their effect on stratospheric chemistry. The 1999-2000 winter was particularly cold, allowing extensive PSC formation. Many trajectories have ten-day periods continuously below the Type I PSC threshold; significant periods of Type II PSCs are also indicated. The model has been used to test the extent and severity of denitrification and dehydration predicted using a range of different microphysical schemes. Scenarios in which freezing only occurs below the ice frost point (causing explicit coupling of denitrification and dehydration) have been tested, as well as scenarios with partial freezing at warmer temperatures (in which denitrification can occur independently of dehydration). The sensitivity to parameters such as aerosol freezing rates and heterogeneous freezing have been explored. Several scenarios cause sufficient denitrification to affect chlorine partitioning, and in turn, model-predicted ozone depletion, demonstrating that an improved understanding of the microphysics responsible for denitrification is necessary for understanding ozone loss rates.

Drdla, Katja↗

Explicit block encodings of boundary value problems for many-body elliptic operators

Simulation of physical systems is one of the most promising use cases of future digital quantum computers. In this work we systematically analyze the quantum circuit complexities of block encoding the discretized elliptic operators that arise extensively in numerical simulations for partial differential equations, including high-dimensional instances for many-body simulations. When restricted to rectangular domains with separable boundary conditions, we provide explicit circuits to block encode the many-body Laplacian with separable periodic, Dirichlet, Neumann, and Robin boundary conditions, using standard discretization techniques from low-order finite difference methods. To obtain high-precision, we introduce a scheme based on periodic extensions to solve Dirichlet and Neumann boundary value problems using a high-order finite difference method, with only a constant increase in total circuit depth and subnormalization factor. We then present a scheme to implement block encodings of differential operators acting on more arbitrary domains, inspired by Cartesian immersed boundary methods. We then block encode the many-body convective operator, which describes interacting particles experiencing a force generated by a pair-wise potential given as an inverse power law of the interparticle distance. This work provides concrete recipes that are readily translated into quantum circuits, with depth logarithmic in the total Hilbert space dimension, that block encode operators arising broadly in applications involving the quantum simulation of quantum and classical many-body mechanics.

Kharazi, Tyler [University of California, Berkeley↗

Stable explicit schemes for equations of Schroedinger type

A method for constructing explicit finite-difference schemes which can be used to solve Schroedinger-type partial-differential equations is presented. A forward Euler scheme that is conditionally stable is given by the procedure. The results presented are based on the analysis of the simplest Schroedinger type equation.

Mickens, Ronald E.↗

Analysis of composite ablators using massively parallel computation

In this work, the feasibility of using massively parallel computation to study the response of ablative materials is investigated. Explicit and implicit finite difference methods are used on a massively parallel computer, the Thinking Machines CM-5. The governing equations are a set of nonlinear partial differential equations. The governing equations are developed for three sample problems: (1) transpiration cooling, (2) ablative composite plate, and (3) restrained thermal growth testing. The transpiration cooling problem is solved using a solution scheme based solely on the explicit finite difference method. The results are compared with available analytical steady-state through-thickness temperature and pressure distributions and good agreement between the numerical and analytical solutions is found. It is also found that a solution scheme based on the explicit finite difference method has the following advantages: incorporates complex physics easily, results in a simple algorithm, and is easily parallelizable. However, a solution scheme of this kind needs very small time steps to maintain stability. A solution scheme based on the implicit finite difference method has the advantage that it does not require very small times steps to maintain stability. However, this kind of solution scheme has the disadvantages that complex physics cannot be easily incorporated into the algorithm and that the solution scheme is difficult to parallelize. A hybrid solution scheme is then developed to combine the strengths of the explicit and implicit finite difference methods and minimize their weaknesses. This is achieved by identifying the critical time scale associated with the governing equations and applying the appropriate finite difference method according to this critical time scale. The hybrid solution scheme is then applied to the ablative composite plate and restrained thermal growth problems. The gas storage term is included in the explicit pressure calculation of both problems. Results from ablative composite plate problems are compared with previous numerical results which did not include the gas storage term. It is found that the through-thickness temperature distribution is not affected much by the gas storage term. However, the through-thickness pressure and stress distributions, and the extent of chemical reactions are different from the previous numerical results. Two types of chemical reaction models are used in the restrained thermal growth testing problem: (1) pressure-independent Arrhenius type rate equations and (2) pressure-dependent Arrhenius type rate equations. The numerical results are compared to experimental results and the pressure-dependent model is able to capture the trend better than the pressure-independent one. Finally, a performance study is done on the hybrid algorithm using the ablative composite plate problem. It is found that there is a good speedup of performance on the CM-5. For 32 CPU's, the speedup of performance is 20. The efficiency of the algorithm is found to be a function of the size and execution time of a given problem and the effective parallelization of the algorithm. It also seems that there is an optimum number of CPU's to use for a given problem.

Shia, David↗

Explicit numerical formulas of improved stability and accuracy for the solution of parabolic equations

A class of explicit numerical formulas which involve next nearest neighbor as well as nearest neighbor points are explored in this paper. These formulas are formal approximations to the linear parabolic partial-differential equation of first order in time and second order in distance. It was found that some of these formulas can employ time steps as much as four times that for the conventional explicit technique without becoming unstable. Others showed improved accuracy for a given time step and spatial grid spacing. One formula achieved a steady-state solution of specified accuracy for an example problem in less than 4 percent of the total computational time required by the conventional explicit technique.

Olstad, W. B.↗

Fast permeability measurement for tight reservoir cores using only initial data of the one chamber pressure pulse decay test

Here, in this study, a mathematical model for fast determination of the permeabilities of tight rocks using measurements taken from the initial period of the One Chamber Pressure Pulse Decay (OC-PPD) test is presented. The model applies to measurements taken both before and after the pressure pulse front has reached the downstream end of the specimen. The analytical solutions for the pressure decay in the upstream chamber are derived based on a parabolic arc approximation of pore pressure distribution along the test specimen. This approximation allows converting the initial–boundary value problem of fluid diffusion in the specimen, governed by partial differential equations, to a system of ordinary differential equations that can be easily solved by explicit formulae. Thus, an explicit formula for the pressure decay rate is obtained, which enables inverse analysis of the initial experimental data to estimate the rock permeability. The proposed method expedites the pulse decay test as it does not require the system to reach equilibrium. The method is validated with three sets of experimental data of the OC-PPD test using helium as the diffusing fluid, for which the relative error of the permeability is found to be less than 6%. This method is particularly useful if the equilibrium time of the pulse decay test for rock specimens with permeabilities in the range of nano-Darcy takes hours or days.

early-time solution↗

Multiscale modeling of HBV infection integrating intra- and intercellular viral propagation to analyze extracellular viral markers

Chronic infection with hepatitis B virus (HBV) is caused by the persistence of closed circular DNA (cccDNA) in the nucleus of infected hepatocytes. Despite available therapeutic anti-HBV agents, eliminating the cccDNA remains challenging. Thus, quantifying and understanding the dynamics of cccDNA are essential for developing effective treatment strategies and new drugs. However, such study requires repeated liver biopsy to measure the intrahepatic cccDNA, which is basically not accepted because liver biopsy is potentially morbid and not common during hepatitis B treatment. We here aimed to develop a noninvasive method for quantifying cccDNA in the liver using surrogate markers in peripheral blood. We constructed a multiscale mathematical model that explicitly incorporates both intracellular and intercellular HBV infection processes. The model, based on age-structured partial differential equations, integrates experimental data from in vitro and in vivo investigations. By applying this model, we roughly predicted the amount and dynamics of intrahepatic cccDNA within a certain range using specific viral markers in serum samples, including HBV DNA, HBsAg, HBeAg, and HBcrAg. Our study represents a significant step towards advancing the understanding of chronic HBV infection. The noninvasive quantification of cccDNA using our proposed method holds promise for improving clinical analyses and treatment strategies. By comprehensively describing the interactions of all components involved in HBV infection, our multiscale mathematical model provides a valuable framework for further research and the development of targeted interventions.

59 BASIC BIOLOGICAL SCIENCES↗

Surrogate modeling of Cellular-Potts agent-based models as a segmentation task using the U-Net neural network architecture

The Cellular-Potts model is a powerful and ubiquitous framework for developing computational models for simulating complex multicellular biological systems. Cellular-Potts models (CPMs) are often computationally expensive due to the explicit modeling of interactions among large numbers of individual model agents and diffusive fields described by partial differential equations (PDEs). In this work, we develop a convolutional neural network (CNN) surrogate model using a U-Net architecture that accounts for periodic boundary conditions. We use this model to accelerate the evaluation of a mechanistic CPM previously used to investigate in vitro vasculogenesis. The surrogate model was trained to predict 100 computational steps ahead (Monte-Carlo steps, MCS), accelerating simulation evaluations by a factor of 562 times compared to single-core CPM code execution on CPU. Over short timescales of up to 3 recursive evaluations, or 300 MCS, our model captures the emergent behaviors demonstrated by the original Cellular-Potts model such as vessel sprouting, extension and anastomosis, and contraction of vascular lacunae. This approach demonstrates the potential for deep learning to serve as a step toward efficient surrogate models for CPM simulations, enabling faster evaluation of computationally expensive CPM simulations of biological processes.

97 MATHEMATICS AND COMPUTING↗

A Primer on Nuclear "Recoil" Data

For many years the ENDF-6 format has existed to contain evaluated nuclear data. One primary driver for the format and the data is neutron transport calculations. Evaluated data can be processed by a code like NJOY into either continuous energy form (ACE format) for Monte Carlo codes like MCNP or into multi-group form (NDI tables) for deterministic codes like Partisn. The reaction cross sections are found in the MF 3 section of the ENDF-6 format. If the reaction produces one or more neutrons as outputs, then secondary neutron data must also be given in MF 4,5 or 6 sections of the format. Energy and angular distributions for the output neutrons must be given in one of several available formats. The most general formats are found in MF 6. MF 4 is for angular distributions, MF 5 is for Energy distributions, and MF 6 contains both. In recent years, more interest has developed in the other output particles (i.e., the “recoil” particles) from neutron induced reactions. This has been driven by interest in charged particle transport and in more specialized partial kermas. ( A separate total neutron kerma has been available for a long time.) Partial kermas are a breakdown of the Kinetic Energy Released into the MAterial by output particle or by neutron reaction. The sum of the partial kermas should be equal to the total kerma on a group-wise basis. The ENDF-6 format is general enough for these new data requirements. Ideally, evaluated data would exist for every output particle (including the secondary neutrons) from every neutron-induced reaction. In the MF 6 format section, data for multi-particle outputs may be entered using the LAW =1 option. This option explicitly allows energy and angular output distributions for each particle produced in the reaction. Such information should preserve the balance between partial kermas and the total kerma at the groupwise level as well as the individual particle averaged energies. For simpler 2-body reactions, LAW = 2 is available. This allows the evaluation to specify only enough data to specify the 2-body reaction fully. Such a simplification does not exist for 3 (or more) body breakups. A simplified form of LAW 2, i.e., LAW 3, also exists to generate approximate recoil output distributions in the absence of full data. However, evaluated data does not generally exist at this fine granularity for reactions involving more than 2 output particles ( e.g., the 3-body break-up reaction). When the multi-body detailed output distribution data is not available, LAW=6 may be employed in NJOY. LAW 6 produces approximate output distributions for all the particles produced in the reaction. Just like in the 2-body case, the smaller particles will generally carry off more energy. At any particular energy, the balance between the sum of the partial kermas and the total kerma will not necessarily be preserved. However, the average energy of each output particle from a reaction is preserved.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗