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Fast DNA sequence alignment using optical computing

Description: Alignment of DNA sequences is a necessary step prior to comparison of sequence data. High-speed alignment is needed due to the large size of DNA databases. Correlation, a standard pattern recognition technique, can be used to perform alignment. Correlation can be performed rapidly using optical techniques. Thus, optical correlation offers the potential for high-speed processing of DNA sequence data. This report describes research efforts to apply one-dimensional acousto-optical correlation methods to the problem of DNA sequence alignment. Experimental results are presented.
Date: November 1, 1996
Creator: Yee, M.L. & Craft, D.C.
Partner: UNT Libraries Government Documents Department

Dispersive water waves in one and two dimensions

Description: This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). We derived and analyzed new shallow water equations for one-dimensional flows near the critical Froude number as well as related integrable systems of evolutionary nonlinear partial differential equations in one spatial dimension, while developing new directions for the mathematics underlying the integrability of these systems. In particular, we applied the spectrum generating equation method to create and study new integrable systems of nonlinear partial differential equations related to our integrable shallow water equations. We also investigated the solutions of these systems of equations on a periodic spatial domain by using methods from the complex algebraic geometry of Riemann surfaces. We developed certain aspects of the required mathematical tools in the course of this investigation, such as inverse scattering with degenerate potentials, asymptotic reduction of the angle representations, geometric singular perturbation theory, modulation theory and singularity tracking for completely integrable equations. We also studied equations that admit weak solutions, i.e., solutions with discontinuous derivatives in the form of comers or cusps, even though they are solutions of integrable models, a property that is often incorrectly assumed to imply smooth solution behavior. In related work, we derived new shallow water equations in two dimensions for an incompressible fluid with a free surface that is moving under the force of gravity. These equations provide an estimate of the long-time asymptotic effects of slowly varying bottom topography and weak hydrostatic imbalance on the vertically averaged horizontal velocity, and they describe the flow regime in which the Froude number is small -- much smaller even than the small aspect ratio of the shallow domain.
Date: August 1, 1997
Creator: Holm, D.D. & Camassa, R.A.
Partner: UNT Libraries Government Documents Department

1-D Equilibrium Discrete Diffusion Monte Carlo

Description: We present a new hybrid Monte Carlo method for 1-D equilibrium diffusion problems in which the radiation field coexists with matter in local thermodynamic equilibrium. This method, the Equilibrium Discrete Diffusion Monte Carlo (EqDDMC) method, combines Monte Carlo particles with spatially discrete diffusion solutions. We verify the EqDDMC method with computational results from three slab problems. The EqDDMC method represents an incremental step toward applying this hybrid methodology to non-equilibrium diffusion, where it could be simultaneously coupled to Monte Carlo transport.
Date: August 2000
Creator: Evans, T. M.; Urbatsch, T. J. & Lichtenstein, H.
Partner: UNT Libraries Government Documents Department

A Reduced Order, One Dimensional Model of Joint Response

Description: As a joint is loaded, the tangent stiffness of the joint reduces due to slip at interfaces. This stiffness reduction continues until the direction of the applied load is reversed or the total interface slips. Total interface slippage in joints is called macro-slip. For joints not undergoing macro-slip, when load reversal occurs the tangent stiffness immediately rebounds to its maximum value. This occurs due to stiction effects at the interface. Thus, for periodic loads, a softening and rebound hardening cycle is produced which defines a hysteretic, energy absorbing trajectory. For many jointed sub-structures, this hysteretic trajectory can be approximated using simple polynomial representations. This allows for complex joint substructures to be represented using simple non-linear models. In this paper a simple one dimensional model is discussed.
Date: November 6, 2000
Partner: UNT Libraries Government Documents Department

A Semi-Analytical Solution for Steady Infiltration in Unsaturated Fractured Rock

Description: A semi-analytical solution is developed for one-dimensional steady infiltration in unsaturated fractured rock. The differential form of the mass conservation equation is integrated to yield an analytical expression relating elevation to a function of capillary pressure and relative permeability of the fracture and rock matrix. Constitutive relationships for unsaturated flow in this analysis are taken from van Genuchten [1980] and Mualem [1976], but alternative relations can also be implemented in the integral solution. Expressions are presented for the liquid saturations and pore velocities in the fracture, matrix, and effective continuum materials as a function of capillary pressure and elevation. Results of the analytical solution are applied to examples of infiltration in fractured rock consisting of both homogeneous and composite (layered) domains. The analytical results are also compared to numerical simulations to demonstrate the use of the analytical solution as a benchmarking tool to address computational issues such as grid refinement.
Date: December 19, 2000
Partner: UNT Libraries Government Documents Department

Renormalized dissipation in the nonconservatively forced Burgers equation

Description: A previous calculation of the renormalized dissipation in the nonconservatively forced one-dimensional Burgers equation, which encountered a catastrophic long-wavelength divergence approximately [k min]-3, is reconsidered. In the absence of velocity shear, analysis of the eddy-damped quasi-normal Markovian closure predicts only a benign logarithmic dependence on kmin. The original divergence is traced to an inconsistent resonance-broadening type of diffusive approximation, which fails in the present problem. Ballistic scaling of renormalized pulses is retained, but such scaling does not, by itself, imply a paradigm of self-organized criticality. An improved scaling formula for a model with velocity shear is also given.
Date: January 19, 2000
Creator: Krommes, J.A.
Partner: UNT Libraries Government Documents Department

One-dimensional, steady compressible flow with friction factor and uniform heat flux at the wall specified

Description: The purpose of this work is to present generalized graphical results to readily permit passage design for monatomic gases, the results including accommodation of any independently specified friction factor, heat transfer coefficient, and wall heat flux. Only constant area passages are considered, and the specified wall heat flux is taken to be uniform.
Date: October 27, 1997
Creator: Landram, C.S.
Partner: UNT Libraries Government Documents Department

Kick and phase errors in spontaneous and amplified radiation.

Description: Two types of magnet errors are considered--the random phase error (RPE), in which the phase errors are evenly distributed along the magnet, and the random kick error (RKE), in which the errors in the derivative of the phase are evenly distributed. We compute the reduction in performance of both spontaneous radiation and high-gain free-electron lasers for both types of errors within the framework of 1-D free-electron laser theory.
Date: August 31, 1999
Creator: Kim, K.-J.
Partner: UNT Libraries Government Documents Department

SEACAS Theory Manuals: Part 1. Problem Formulation in Nonlinear Solid Mechancis

Description: This report gives an introduction to the basic concepts and principles involved in the formulation of nonlinear problems in solid mechanics. By way of motivation, the discussion begins with a survey of some of the important sources of nonlinearity in solid mechanics applications, using wherever possible simple one dimensional idealizations to demonstrate the physical concepts. This discussion is then generalized by presenting generic statements of initial/boundary value problems in solid mechanics, using linear elasticity as a template and encompassing such ideas as strong and weak forms of boundary value problems, boundary and initial conditions, and dynamic and quasistatic idealizations. The notational framework used for the linearized problem is then extended to account for finite deformation of possibly inelastic solids, providing the context for the descriptions of nonlinear continuum mechanics, constitutive modeling, and finite element technology given in three companion reports.
Date: August 1, 1998
Creator: Attaway, S.W.; Laursen, T.A. & Zadoks, R.I.
Partner: UNT Libraries Government Documents Department

Approximate Near-Field Blast Theory: A Generalized Approach

Description: A method for analyzing strong shock waves in arbitrary one-dimensional geometry is presented. An approximation to classical Taylor-Sedov theory is extended to the near-field case where source mass is not negligible, accounting for differences in the chemical properties of the source mass and ambient medium. Results from example calculations are compared with previously published analytical formulae.
Date: October 25, 1999
Creator: Hutchens, G.J.
Partner: UNT Libraries Government Documents Department

Magnetoresistance of One-Dimensional Subbands in Tunnel-Coupled Double Quantum Wires

Description: The authors study the low-temperature in-plane magnetoresistance of tunnel-coupled quasi-one-dimensional quantum wires. The wires are defined by two pairs of mutually aligned split gates on opposite sides of a {le} 1 micron thick AlGaAs/GaAs double quantum well heterostructure, allowing independent control of the width of each quantum well. In the ballistic regime, when both wires are defined and the field is perpendicular to the current, a large resistance peak at {approximately}6 Tesla is observed with a strong gate voltage dependence. The data is consistent with a counting model whereby the number of subbands crossing the Fermi level changes with field due to the formation of an anticrossing in each pair of 1D subbands.
Date: August 4, 1999
Creator: Moon, J.S.; Blount, M.A.; Simmons, J.A.; Wendt, J.R.; Lyo, S.K. & Reno, J.L.
Partner: UNT Libraries Government Documents Department

Research and Development Data to Define the Thermal Performance of Reflective Materials Used to Conserve Energy in Building Applications

Description: A comprehensive experimental laboratory study has been conducted on the thermal performance of reflective insulation systems. The goal of this study was to develop test and evaluation protocols and to obtain thermal performance data on a selected number of idealized and commercial systems containing reflective airspaces for use in analytical models. Steady-state thermal resistance has been measured on 17 different test panels using two guarded hot boxes. Additional instrumentation was installed to measure the temperature of critical locations inside the test panels. The test parameters which have been studied are heat flow direction (horizontal, up, and down), number of airspaces comprising the cavity, airspace effective emittance, airspace aspect ratio, airspace mean temperature and temperature difference, and the thermal resistance of the stud material. Tests have also been performed on similar constructions with mass insulation. Two one-dimensional calculation techniques (ASHRAE and proposed ASTM) have been employed to determine the cavity thermal resistance from the measured test panel results. The measured cavity thermal resistance is compared with literature data which is commonly employed to calculate the thermal resistance of reflective airspace assemblies. A consumer-oriented handbook pertaining to reflective insulation for building and commercial applications has also been prepared as part of this study.
Date: April 9, 2001
Creator: Eisenberg, J
Partner: UNT Libraries Government Documents Department

Local One-Dimensional ICRF Full-Wave Solutions Valid to All Orders in k-Perpendicular-Rho

Description: High harmonic ion cyclotron resonances are important for understanding future fast wave heating experiments on NSTX 1 as well as recent ICRF flow drive experiments on PBX-M<sup>2</sup> and TFTR<sup>3</sup>. Unfortunately, many of our ICRF wave analysis codes are based on an expansion to second order in k-perpendicular-Rho where k-perpendicular is the perpendicular wave number, and Rho is the Larmor radius. Such codes are limited to cyclotron harmonics less than or equal to 2. Integral codes<sup>4,5</sup> on the other hand, are valid to all orders in both k-perpendicular-Rho and Rho/<i>L</i>L where <i>L</i> is the equilibrium scale length. But velocity space integrals in these codes require long running times. Here we take a simpler approach which assumes a local plasma conductivity (Rho/<i>L</i> << 1), while still retaining all orders in k-perpendicular-Rho. This allows high harmonic fast wave and flow drive applications, while requiring less computing time than conventional integral codes.
Date: April 12, 1999
Creator: Batchelor, D.B.; Berry, L.A. & Jaeger, E.F.
Partner: UNT Libraries Government Documents Department


Description: Accurate simulation of in-situ combustion processes is computationally very challenging because the spatial and temporal scales over which the combustion process takes place are very small. In this first quarterly report of our DoE funded research, we discuss the design of a new simulation tool based on an efficient Cartesian Adaptive Mesh Refinement technique that allows much higher grid densities to be used near typical fronts than current simulators. The formulation presented here for a first one-dimensional simulator will serve as the foundation for the development of a three-dimensional simulator that can handle realistic permeability heterogeneity. The development of the simulation tool will be supported by extensive laboratory experiments conducted to provide validation data, and to study effective variants of the combustion process. The preliminary investigation reported here shows how metallic salt additives can promote and sustain combustion by enhancing the oxidation and cracking of hydrocarbons.
Date: April 1, 2004
Creator: Gerritsen, Margot & Kovscek, Anthony R.
Partner: UNT Libraries Government Documents Department

Evolution of flow disturbances in cocurrent gas-liquid flows. Final report, November 1, 1993--October 31, 1994

Description: Long-wave stability curves for two-layer laminar flow, laminar liquid and a turbulent gas (simulated with a polynomial profile) from the full differential equations and boundary conditions are compared to the standard 1-d equation methods of predicting flow regime transitions. The differential models predict instability at much less severe conditions than the integral equations -- as much as an order of magnitude when plotted on friction velocity -- liquid depth coordinates. Since this plot removes most of the base state`s effects, the 1-d models clearly are not predicting linear stability of anything. So agreement between the 1-d models with observed transitions is fortuitous since either the flow is too short or convenient parameter values have been chosen; otherwise flow regimes are not linked with linear stability. A polynomial profile gas, laminar liquid model, developed for a first approximation to turbulent flow, gives growth curves near the two-layer laminar exact solutions if the interfacial friction velocity and liquid depth are matched. The main differences are that the wavelength is predicted somewhat shorter for the turbulent model and the growth rate slightly larger for a laminar gas. These linear stability studies point to a need to determine the base state before significant results are obtained. Solutions for laminar flow in a rectangular channel over a solid wavy surface show that the wavelength/channel height ratio profoundly affects the stress variations. For waves long compared to channel height, pressure is completely in phase with wave slope, not wave height, as occurs for high Re in infinitely high channels. Nonlinear effects reduce the relative magnitude of the shear stress variation and phase angle that could explain saturation in the growth of waves formed by shear variation for very thin liquid layers. But since the pressure variation and phase are increased, this is not a likely explanation ...
Date: December 1, 1994
Creator: McCready, M. J.
Partner: UNT Libraries Government Documents Department

Nonstandard Analysis and Shock Wave Jump Conditions in a One-Dimensional Compressible Gas

Description: Nonstandard analysis is a relatively new area of mathematics in which infinitesimal numbers can be defined and manipulated rigorously like real numbers. This report presents a fairly comprehensive tutorial on nonstandard analysis for physicists and engineers with many examples applicable to generalized functions. To demonstrate the power of the subject, the problem of shock wave jump conditions is studied for a one-dimensional compressible gas. It is assumed that the shock thickness occurs on an infinitesimal interval and the jump functions in the thermodynamic and fluid dynamic parameters occur smoothly across this interval. To use conservations laws, smooth pre-distributions of the Dirac delta measure are applied whose supports are contained within the shock thickness. Furthermore, smooth pre-distributions of the Heaviside function are applied which vary from zero to one across the shock wave. It is shown that if the equations of motion are expressed in nonconservative form then the relationships between the jump functions for the flow parameters may be found unambiguously. The analysis yields the classical Rankine-Hugoniot jump conditions for an inviscid shock wave. Moreover, non-monotonic entropy jump conditions are obtained for both inviscid and viscous flows. The report shows that products of generalized functions may be defined consistently using nonstandard analysis; however, physically meaningful products of generalized functions must be determined from the physics of the problem and not the mathematical form of the governing equations.
Date: May 25, 2007
Creator: Roy S. Baty, F. Farassat, John A. Hargreaves
Partner: UNT Libraries Government Documents Department

Reliable estimation of shock position in shock-capturing compressible hydrodynamics codes

Description: The displacement method for estimating shock position in a shock-capturing compressible hydrodynamics code is introduced. Common estimates use simulation data within the captured shock, but the displacement method uses data behind the shock, making the estimate consistent with and as reliable as estimates of material parameters obtained from averages or fits behind the shock. The displacement method is described in the context of a steady shock in a one-dimensional lagrangian hydrodynamics code, and demonstrated on a piston problem and a spherical blast wave.The displacement method's estimates of shock position are much better than common estimates in such applications.
Date: January 1, 2008
Creator: Nelson, Eric M
Partner: UNT Libraries Government Documents Department

Hard superconducting materials. Final report

Description: During the period covered by this program (1962-1971). extensive studies of the material parameters and mechanisms controlling critical currents, flux creep and inreversiblity in hand superconducting materials were carried out. Quantitative theories of the pinning and creep processes were developed and tested extensively using equipment and methods developed locally. The role of the superconducting surface sheath was explored in detail and somewhat similar phenomena were found to operate there. The superconducting quantum interferrometry developed for the creep studies proved to be an extremely valuable tool in the study of quantum fluctuations in one-dimensional superconductors. Inltial attempts to study the flux structure by low temperature electron microscopy proved non-productive but later studies using the Bitter pattern technique of Trauble and Essmann were of value fn the study of the flux structure transitions in thin films. Development of instrumentation based on superconducting technology such as a femtovoltmeter and practicable point contact flux detectons also arose under the program. A list of publications is appended. ( auth)
Date: January 1, 1973
Creator: Silcox, J. & Webb, W.W.
Partner: UNT Libraries Government Documents Department

Preliminary analysis of core capsule x-ray spectroscopy and image results for medium-to-high growth factor implosions

Description: Recent capsule implosions using indirect drive on NOVA have probed core and near-core capsule T{sub e}, {rho} and mix structure using non-trivial pulse shapes (i.e. with a foot). These experiments have been performed using smooth as well as artificially roughened capsules. They have been performed using basically 3 non-trivial pulse-shapes with 3 different types of capsules with correspondingly different growth regimes for Rayleigh-Taylor instabilities. These experiments have employed time-dependent spectroscopy, gated imaging and absolutely calibrated time-integrated imaging as x-ray diagnostics. The authors compare nominal and {open_quotes}modified{close_quotes} 1D calculations with the spectroscopic and time-integrated image results. They find that the core T{sub e} is less than calculated (not surprising), but also that the T{sub e} of the inner pusher is substantially higher (at least 20%) than predicted, with perhaps some enhanced mix of the PVA layer towards the core.
Date: September 1, 1995
Creator: Pollak, G.; Delamater, N. & Landen, N.
Partner: UNT Libraries Government Documents Department

Simulations of core collapse supernovae in one and two dimensions using multigroup neutrino transport

Description: In one dimension, we present results from comparisons of stationary state multi-group flux-limited diffusion and Boltzmann neutrino transport, focusing on quantities central to the postbounce shock reheating. In two dimensions, we present results from simulations that couple one-dimensional multigroup flux-limited diffusion to two- dimensional (PPM) hydrodynamics.
Date: December 31, 1996
Creator: Mezzacappa, A.
Partner: UNT Libraries Government Documents Department

Time-domain solutions for nonlinear elastic 1-D plane wave propagation

Description: Time-domain solutions are obtained for 1-D nonlinear elastic wave propagation problems using a five-constant nonlinear theory. The assumption of weak attenuation was used throughout the development. The strongest nonlinear effects are obtained for the case of single compressional wave propagation, for single compressional or shear wave propagation through a longitudinally pre-stressed elastic material, and for shear wave propagation in a shear pre-stressed elastic material. Estimates of the size of these effects indicate that nonlinear phenomena are likely to be observable in real seismic data. The results may be useful for the measurement of nonlinear constants in elastic materials, for explaining the frequency content of seismograms, and for monitoring strain fields in the earth`s crust.
Date: June 1, 1998
Creator: Korneev, V.A.
Partner: UNT Libraries Government Documents Department