Showing papers by "Sandia National Laboratories published in 1998"

Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

Abstract: A novel and robust automated docking method that predicts the bound conformations of flexible ligands to macromolecular targets has been developed and tested, in combination with a new scoring function that estimates the free energy change upon binding. Interestingly, this method applies a Lamarckian model of genetics, in which environmental adaptations of an individual's phenotype are reverse transcribed into its genotype and become . heritable traits sic . We consider three search methods, Monte Carlo simulated annealing, a traditional genetic algorithm, and the Lamarckian genetic algorithm, and compare their performance in dockings of seven protein)ligand test systems having known three-dimensional structure. We show that both the traditional and Lamarckian genetic algorithms can handle ligands with more degrees of freedom than the simulated annealing method used in earlier versions of AUTODOCK, and that the Lamarckian genetic algorithm is the most efficient, reliable, and successful of the three. The empirical free energy function was calibrated using a set of 30 structurally known protein)ligand complexes with experimentally determined binding constants. Linear regression analysis of the observed binding constants in terms of a wide variety of structure-derived molecular properties was performed. The final model had a residual standard y1 y1 .

Dislocation nucleation and defect structure during surface indentation

Abstract: We model indentation of a metal surface by combining an atomistic metal with a hard-sphere indenter. This work provides atomistic imaging of dislocation nucleation during displacement controlled indentation on a passivated surface. Dislocations and defects are located and imaged by local deviations from centrosymmetry. For a Au(111) surface, nucleation of partial dislocation loops occurs below the surface inside the indenter contact area. We compare and contrast these observations with empirical criteria for dislocation nucleation and corresponding continuum elasticity solutions.

A three-dimensional photonic crystal operating at infrared wavelengths

Abstract: The ability to confine and control light in three dimensions would have important implications for quantum optics and quantum-optical devices: the modification of black-body radiation, the localization of light to a fraction of a cubic wavelength, and thus the realization of single-mode light-emitting diodes, are but a few examples1,2,3. Photonic crystals — the optical analogues of electronic crystal — provide a means for achieving these goals. Combinations of metallic and dielectric materials can be used to obtain the required three-dimensional periodic variations in dielectric constant, but dissipation due to free carrier absorption will limit application of such structures at the technologically useful infrared wavelengths4. On the other hand, three-dimensional photonic crystals fabricated in low-loss gallium arsenide show only a weak ‘stop band’ (that is, range of frequencies at which propagation of light is forbidden) at the wavelengths of interest5. Here we report the construction of a three-dimensional infrared photonic crystal on a silicon wafer using relatively standard microelectronics fabrication technology. Our crystal shows a large stop band (10–14.5 μm), strong attenuation of light within this band (∼12 dB per unit cell) and a spectral response uniform to better than 1 per cent over the area of the 6-inch wafer.

Solar Wind Electron Proton Alpha Monitor (SWEPAM) for the Advanced Composition Explorer

Abstract: The Solar Wind Electron Proton Alpha Monitor (SWEPAM) experiment provides the bulk solar wind observations for the Advanced Composition Explorer (ACE). These observations provide the context for elemental and isotopic composition measurements made on ACE as well as allowing the direct examination of numerous solar wind phenomena such as coronal mass ejections, interplanetary shocks, and solar wind fine structure, with advanced, 3-D plasma instrumentation. They also provide an ideal data set for both heliospheric and magnetospheric multi-spacecraft studies where they can be used in conjunction with other, simultaneous observations from spacecraft such as Ulysses. The SWEPAM observations are made simultaneously with independent electron and ion instruments. In order to save costs for the ACE project, we recycled the flight spares from the joint NASA/ESA Ulysses mission. Both instruments have undergone selective refurbishment as well as modernization and modifications required to meet the ACE mission and spacecraft accommodation requirements. Both incorporate electrostatic analyzers whose fan-shaped fields of view sweep out all pertinent look directions as the spacecraft spins. Enhancements in the SWEPAM instruments from their original forms as Ulysses spare instruments include (1) a factor of 16 increase in the accumulation interval (and hence sensitivity) for high energy, halo electrons; (2) halving of the effective ion-detecting CEM spacing from ∼5° on Ulysses to ∼2.5° for ACE; and (3) the inclusion of a 20° conical swath of enhanced sensitivity coverage in order to measure suprathermal ions outside of the solar wind beam. New control electronics and programming provide for 64-s resolution of the full electron and ion distribution functions and cull out a subset of these observations for continuous real-time telemetry for space weather purposes.

A graph-based system for network-vulnerability analysis

Abstract: This paper presents a graph-based approach to network vulnerability analysis. The method is flexible, allowing analysis of attacks from both outside and inside the network. It can analyze risks to a specific network asset, or examine the universe of possible consequences following a successful attack. The graph-based tool can identify the set of attack paths that have a high probability of success (or a low effort cost) for the attacker. The system could be used to test the effectiveness of making configuration changes, implementing an intrusion detection system, etc. The analysis system requires as input a database of common attacks, broken into atomic steps, specific network configuration and topology information, and an attacker profile. The attack information is matched with the network configuration information and an attacker profile to create a superset attack graph. Nodes identify a stage of attack, for example the class of machines the attacker has accessed and the user privilege level he or she has compromised. The arcs in the attack graph represent attacks or stages of attacks. By assigning probabilities of success on the arcs or costs representing level-of-effort for the attacker, various graph algorithms such as shortest-path algorithms can identify the attack paths with the highest probability of success.

Stringlike cooperative motion in a supercooled liquid

Abstract: Extensive molecular dynamics simulations are performed on a glass-forming Lennard-Jones mixture to determine the nature of the cooperative motions occurring in this model fragile liquid. We observe stringlike cooperative molecular motion (``strings'') at temperatures well above the glass transition. The mean length of the strings increases upon cooling, and the string length distribution is found to be nearly exponential.

Effects of turbulence on species mass fractions in methane/air jet flames

Abstract: It is important that combustion models capture the effects of turbulent mixing on reaction zone structure in non-premixed and partially premixed flames. A more complete understanding of the response of species mass fractions to turbulent mixing is needed to improve predictive capabilities, particularly with regard to combustion intermediates and minor species. Using the combination of Raman scattering. Rayleigh scattering, and laser-induced fluorescence, simultaneous measurements of CO, OH, H2, and NO are obtained along with the major species, temperature, and mixture fraction in a series of six piloted methane/air jet flames. Flame conditions vary from laminar to turbulent with significant localized extinction. Two-photon laser-induced fluorescence (TPLIF) is used to determine instantaneous CO concentrations, providing an improvement over Raman scattering measurements of CO in methane flames. Conditional probability density functions (cpdf's) of species mass fractions in the six flames are compared. Significant changes are observed in the mass fraction cpdf's of several species. Results for H2O, CO2, H2, and OH are consistent with the concept that turbulent transport becomes dominant over molecular diffusion within the range of Reynolds numbers and axial locations considered in these experiments. The cpdf's of CO mass fraction are broadened in the turbulent flames relative to the laminar flame. However, there is not an increase in the maximum conditional mean value of the CO mass fraction as suggested by some previously reported measurements in methane flames. The cpdf's of NO mass fraction at a given streamwise location in the turbulent flames show NO levels decreasing significantly as jet velocity increases.

Gas Dynamic Principles of Cold Spray

Abstract: This paper presents an analytical model of the cold-spray process. By assuming a one-dimensional isentropic flow and constant gas properties, analytical equations are solved to predict the spray particle velocities. The solutions demonstrate the interaction between the numerous geometric and material properties. The analytical results allow determination of an optimal design for a cold-spray nozzle. The spray particle velocity is determined to be a strong function of the gas properties, particle material density, and size. It is also shown that the system performance is sensitive to the nozzle length, but not sensitive to the nozzle shape. Thus, it is often possible to use one nozzle design for a variety of operational conditions. Many of the results obtained in this article are also directly applicable to other thermal spray processes.

On enabling secure applications through off-line biometric identification

Abstract: In developing secure applications and systems, designers must often incorporate secure user identification in the design specification. In this paper, we study secure off-line authenticated user identification schemes based on a biometric system that can measure a user's biometrics accurately (up to some Hamming distance). The presented schemes enhance identification and authorization in secure applications by binding a biometric template with authorization information on a token such as a magnetic strip. Also developed are schemes specifically designed to minimize the compromising of a user's private biometrics data, encapsulated in the authorization information, without requiring secure hardware tokens. We also study the feasibility of biometrics performing as an enabling technology for secure systems and applications design. We investigate a new technology which allows a user's biometrics to facilitate cryptographic mechanisms.

Photoluminescence from nanosize gold clusters

Abstract: We have observed visible light emission from nanosize gold clusters. Liquid chromatographic analysis of the metal clusters shows that relatively intense photoluminescence occurs only when the size of the metal nanocluster is sufficiently small (<5 nm). The emission is strongly Stokes shifted and is assigned to radiative recombination of Fermi level electrons and sp- or d-band holes. The electron and/or hole states are perturbed by surface states, as indicated by the dependence of the emission spectrum on the nature of the cluster surface. Finally, we found that large, nonemitting gold clusters can also be made luminescent by partial dissolution using KCN.

A comparison of select trigger algorithms for automated global seismic phase and event detection

Abstract: Digital algorithms for robust detection of phase arrivals in the presence of stationary and nonstationary noise have a long history in seismology and have been exploited primarily to reduce the amount of data recorded by data logging systems to manageable levels. In the present era of inexpensive digital storage, however, such algorithms are increasingly being used to flag signal segments in continuously recorded digital data streams for subsequent processing by automatic and/or expert interpretation systems. In the course of our development of an automated, near-real-time, waveform correlation event-detection and location system (WCEDS), we have surveyed the abilities of such algorithms to enhance seismic phase arrivals in teleseismic data streams. Specifically, we have considered envelopes generated by energy transient (STA/LTA), Z -statistic, frequency transient, and polarization algorithms. The WCEDS system requires a set of input data streams that have a smooth, low-amplitude response to background noise and seismic coda and that contain peaks at times corresponding to phase arrivals. The algorithm used to generate these input streams from raw seismograms must perform well under a wide range of source, path, receiver, and noise scenarios. Present computational capabilities allow the application of considerably more robust algorithms than have been historically used in real time. However, highly complex calculations can still be computationally prohibitive for current workstations when the number of data streams become large. While no algorithm was clearly optimal under all source, receiver, path, and noise conditions tested, an STA/LTA algorithm incorporating adaptive window lengths controlled by nonstationary seismogram spectral characteristics was found to provide an output that best met the requirements of a global correlation-based event-detection and location system.

A Lattice-Boltzmann Method for Partially Saturated Computational Cells

Abstract: The lattice-Boltzmann (LB) method is applied to complex, moving geometries in which computational cells are partially filled with fluid. The LB algorithm is modified to include a term that depends on the percentage of the cell saturated with fluid. The method is useful for modeling suspended obstacles that do not conform to the grid. Another application is to simulations of flow through reconstructed media that are not easily segmented into solid and liquid regions. A detailed comparison is made with FIDAP simulation results for the flow about a periodic line of cylinders in a channel at a non-zero Reynolds number. Two cases are examined. In the first simulation, the cylinders are given a constant velocity along the axis of the channel, and the steady solution is acquired. The transient behavior of the system is then studied by giving the cylinders an oscillatory velocity. For both steady and oscillatory flows, the method provides excellent agreement with FIDAP simulation results, even at locations close ...

A common language for computer security incidents

Abstract: Much of the computer security information regularly gathered and disseminated by individuals and organizations cannot currently be combined or compared because a common language has yet to emerge in the field of computer security. A common language consists of terms and taxonomies (principles of classification) which enable the gathering, exchange and comparison of information. This paper presents the results of a project to develop such a common language for computer security incidents. This project results from cooperation between the Security and Networking Research Group at the Sandia National Laboratories, Livermore, CA, and the CERT{reg_sign} Coordination Center at Carnegie Mellon University, Pittsburgh, PA. This Common Language Project was not an effort to develop a comprehensive dictionary of terms used in the field of computer security. Instead, the authors developed a minimum set of high-level terms, along with a structure indicating their relationship (a taxonomy), which can be used to classify and understand computer security incident information. They hope these high-level terms and their structure will gain wide acceptance, be useful, and most importantly, enable the exchange and comparison of computer security incident information. They anticipate, however, that individuals and organizations will continue to use their own terms, which may be more specific both in meaning and use. They designed the common language to enable these lower-level terms to be classified within the common language structure.

A comparison of seven geostatistically based inverse approaches to estimate transmissivities for modeling advective transport by groundwater flow

Abstract: This paper describes the first major attempt to compare seven different inverse approaches for identifying aquifer transmissivity. The ultimate objective was to determine which of several geostatistical inverse techniques is better suited for making probabilistic forecasts of the potential transport of solutes in an aquifer where spatial variability and uncertainty in hydrogeologic properties are significant. Seven geostatistical methods (fast Fourier transform (FF), fractal simulation (FS), linearized cokriging (LC), linearized semianalytical )LS), maximum likelihood (ML), pilot point (PP), and sequential self-calibration (SS)) were compared on four synthetic data sets. Each data set had specific features meeting (or not) classical assumptions about stationarity, amenability to a geostatistical description, etc. The comparison of the outcome of the methods is based on the prediction of travel times and travel paths taken by conservative solutes migrating in the aquifer for a distance of 5 km. Four of the methods, LS, ML, PP, and SS, were identified as being approximately equivalent for the specific problems considered. The magnitude of the variance of the transmissivity fields, which went as high as 10 times the generally accepted range for linearized approaches, was not a problem for the linearized methods when applied to stationary fields; that is, their inverse solutions and travel time predictions were as accurate as those of the nonlinear methods. Nonstationarity of the “true” transmissivity field, or the presence of “anomalies” such as high-permeability fracture zones was, however, more of a problem for the linearized methods. The importance of the proper selection of the semivariogram of the log10 (T) field (or the ability of the method to optimize this variogram iteratively) was found to have a significant impact on the accuracy and precision of the travel time predictions. Use of additional transient information from pumping tests did not result in major changes in the outcome. While the methods differ in their underlying theory, and the codes developed to implement the theories were limited to varying degrees, the most important factor for achieving a successful solution was the time and experience devoted by the user of the method.

Enhancement of X-Ray Power from a Z Pinch Using Nested-Wire Arrays

Abstract: Nested-wire arrays on the 20-MA Z -pinch accelerator have produced x-ray powers up to 280{plus_minus}40 TW (a 40{percent} increase over a single array) and an x-ray pulse width of 4thinspthinspns. The short x-ray pulse widths are associated with the formation of tight (1-mm-diameter), uniform pinches at stagnation. Two-dimensional radiation magnetohydrodynamic calculations suggest that the inner array mitigates the growth of implosion instabilities thereby leading to smaller diameter pinches that radiate at higher power than single-wire arrays. {copyright} {ital 1998} {ital The American Physical Society }

Raman Spectroscopy Study of the Structure of Lithium and Sodium Ultraphosphate Glasses

Abstract: Anhydrous binary phosphate glasses containing from 0 to 50 mol% Li2O or Na2O have been prepared and examined by Raman scattering spectroscopy. The unpolarized Raman spectrum of vitreous P2O5 has intense bands near 640 cm−1, attributed to the symmetric stretching mode of POP bridging oxygens, (POP)sym, between Q3 phosphate tetrahedra, and at 1390 cm−1 due to the symmetric stretch of the PO terminal oxygens, (PO)sym. With the addition of alkali oxide to P2O5, a new feature appears in the Raman spectra near 1160 cm−1 indicating the formation of Q2 phosphate tetrahedra with two bridging and two non-bridging oxygens. The increase in relative amplitude of this new (PO2)sym band with increasing modifier content is consistent with a simple depolymerization of the phosphate network. From 20 to 50 mol% alkali oxide, the position of the (PO)sym Raman band decreases by ∼ 130 cm−1 whereas the frequency of the (POP)sym band increases by ∼ 60 cm−1. These frequency shifts are the result of π-bond delocalization on Q3 species that effectively lengthens the PO terminal oxygen bond and strengthens the POP linkages with increasing alkali oxide content. The compositional dependence of the π-bond delocalization on Q3 tetrahedra is described by considering the interconnections between neighboring Q3 and Q2 tetrahedra. The onset of π-bond delocalization on Q3 species corresponds with the anomalous Tg minimum at 20 mol% alkali oxide in alkali ultraphosphate glasses. The increase in Tg between 20 and 50 mol% alkali oxide is attributed to the increased ionic interconnection of what becomes a chain-like phosphate network at higher alkali contents. Finally, the Raman spectra of several alkali ultraphosphate glasses show high frequency shoulders on the Raman bands attributed to the (PO2)sym and (PO2)asym vibrational modes. These shoulders represent the presence of strained structural units, possibly three- or four-membered rings.

New organic materials suitable for use in chemical sensor arrays

Abstract: : In this paper we discuss several different approaches for preparing chemically sensitive interfaces suitable for array-based chemical sensing applications. The characteristics of all these materials are that they are simple to prepare, synthetically versatile, easy to immobilize on transducer surfaces, exhibit chemical class selectivity to a significant extent, provide rapid (and in most cases fully reversible) responses to analytes, and are relatively durable and inexpensive. The first class of surface coatings are organomercaptan self-assembled monolayers (SAMs) terminated in chemically sensitive functional groups. The second class are bilayers prepared by modifying the aforementioned SAMs with either metal ions or calixNarenes. Dendritic polymers confined to surfaces comprise the final class of chemically sensitive interfacial materials. In addition to the synthesis of these materials, we provide ex-situ and in-situ characterization of their structure and chemical properties as well as their interactions with selected analytes using surface-infrared spectroscopy, surface acoustic wave (SAW) device-based gravimetry, and X-ray photoelectron spectroscopy.

Planar laser-induced fluorescence imaging of flame heat release rate

Abstract: Local heat release rate represents one of the most interesting experimental observables in the study of unsteady reacting flows. The direct measure of burning or heat release rate as a field variable is not possible. Numerous experimental investigations have relied on inferring this type of information as well as flame-front topology from indirect measures that are presumed to be correlated. A recent study has brought into question many of the commonly used flame-front marker and burning-rate diagnostics. This same study found that the concentration of formyl radical offers the best possibility for measuring flame burning rate. However, primarily due to low concentrations, the fluorescence signal level from formyl is too weak to employ this diagnostic for single-pulse measurements of turbulent-reacting flows. In this paper, we describe and demonstrate a new fluorescence-based reaction-front imaging diagnostic suitable for single-shot applications. The measurement is based on taking the pixel-by-pixel product of OH and CH2O planar laser-induced fluorescence (PLIF) images to yield an image closely related to a reaction rate. The spectroscopic and collisional processes affecting the measured signals are discussed, and the foundation of the diagnostic, as based on laminar and unsteady flame calculations, is presented. We report the results of applying this diagnostic to the study of a laminar premixed flame subject to an interaction with an isolated line-vortex pair.

Imaging of Pressure- and Electrokinetically Driven Flows through Open Capillaries.

Abstract: A new tool for imaging both scalar transport and velocity fields in liquid flows through microscale structures is described. The technique employs an ultraviolet laser pulse to write a pattern into the flow by uncaging a fluorescent dye. This is followed, at selected time delays, by flood illumination with a pulse of visible light which excites the uncaged dye. The resulting fluorescence image is collected onto a sensitive CCD camera. The instrument is designed as an oil immersion microscope to minimize beam steering effects. The caged fluorescent dye is seeded in trace quantities throughout the active fluid, thus images with high contrast and minimal distortion due to any molecular diffusion history can be obtained at any point within the microchannel by selectively activating the dye in the immediate region of interest. We report images of pressure- and electrokinetically driven steady flow within round cross section capillaries having micrometer scale inner diameters. We also demonstrate the ability to recover the velocity profile from a time sequence of these scalar images by direct inversion of the conserved scalar advection-convection equation.