In theory, it should be possible to infer realistic genetic networks from time series microarray data. In practice, however, network discovery has proved problematic. The three major challenges are: (1) inferring the network; (2) estimating the stability of the inferred network; and (3) making the network visually accessible to the user. Here we describe a method, tested on publicly available time series microarray data, which addresses these concerns. The inference of genetic networks from genome-wide experimental data is an important biological problem which has received much attention. Approaches to this problem have typically included application of clustering algorithms [6]; the use of Boolean networks [12, 1, 10]; the use of Bayesian networks [8, 11]; and the use of continuous models [21, 14, 19]. Overviews of the problem and general approaches to network inference can be found in [4, 3]. Our approach to network inference is similar to earlier methods in that we use both clustering and Boolean network inference. However, we have attempted to extend the process to better serve the end-user, the biologist. In particular, we have incorporated a system to assess the reliability of our network, and we have developed tools which allow interactive visualization of the proposed network.
Khan, Feroz H.; Vannoni, Michael G.; Rajen, Gaurav
India and Pakistan have created sizeable ballistic missile forces and are continuing to develop and enlarge them. These forces can be both stabilizing (e.g., providing a survivable force for deterrence) and destabilizing (e.g., creating strategic asymmetries). Missile forces will be a factor in bilateral relations for the foreseeable future, so restraint is necessary to curtail their destabilizing effects. Such restraint, however, must develop within an atmosphere of low trust. This report presents a set of political and operational options, both unilateral and bilateral, that decreases tensions, helps rebuild the bilateral relationship, and prepares the ground for future steps in structural arms control. Significant steps, which build on precedents and do not require extensive cooperation, are possible despite strained relations. The approach is made up of three distinct phases: (1) tension reduction measures, (2) confidence building measures, and (3) arms control agreements. The goal of the first phase is to initiate unilateral steps that are substantive and decrease tensions, establish missiles as a security topic for bilateral discussion, and set precedents for limited bilateral cooperation. The second phase would build confidence by expanding current bilateral security agreements, formalizing bilateral understandings, and beginning discussion of monitoring procedures. The third phase could include bilateral agreements limiting some characteristics of national missile forces including the cooperative incorporation of monitoring and verification.
Pb deposition on Cu(111) causes the surface to self-assemble into periodically arranged domains of a Pb-rich phase and a Pb-poor phase. Using low-energy electron microscopy (LEEM) we provide evidence that the observed temperature-dependent periodicity of these self-assembled domain patterns is the result of changing domain-boundary free energy. We determine the free energy of boundaries at different temperatures from a capillary wave analysis of the thermal fluctuations of the boundaries and find that it varies from 22 meV/nm at 600 K to 8 meV/nm at 650 K. Combining this result with previous measurements of the surface stress difference between the two phases we find that the theory of surface-stress-induced domain formation can quantitatively account for the observed periodicities.
A technique for manufacturing wires with imposed modulation in radius with axial wavelengths as short as 1 mm is presented. Extruded aluminum 5056 with 15 {micro}m diameter was masked and chemically etched to reduce the radius by {approx}20% in selected regions. Characterized by scanning electron microscopy, the modulation in radius is a step function with a {approx}10 {micro}m wide conical transition between thick and thin segments, with some pitting in etched regions. Techniques for mounting and aligning these wires in arrays for fast z-pinch experiments will be discussed. Axially mass-modulated wire arrays of this type will allow the study of seeded Rayleigh-Taylor instabilities in z pinches, corona formation, wire initiation with varying current density in the wire core, and correlation of perturbations between adjacent wires. This tool will support magnetohydrodynamics code validation in complex three-dimensional geometries, and perhaps x-ray pulse shaping.
We use low-energy electron microscopy to study the mechanisms of thermal smoothing on Rh(001) surfaces at high temperature. By examining the change of areas of two-dimensional islands as a function of time and temperature, we find that smoothing from 1210 K to 1450 K is limited by the rate of surface diffusion on terraces and not by bulk vacancy diffusion as observed in other systems in the same temperature range. However, the activation energy we measure for island decay is inconsistent with previous measurements and calculations of the activation energy of surface diffusion and the adatom formation energy. This inconsistency combined with an unexpectedly large activation entropy suggests a surface transport mechanism other than simple hopping of adatoms across the surface.
This report documents the efforts and accomplishments of the LIGA electrodeposition modeling project which was headed by the ASCI Materials and Physics Modeling Program. A multi-dimensional framework based on GOMA was developed for modeling time-dependent diffusion and migration of multiple charged species in a dilute electrolyte solution with reduction electro-chemical reactions on moving deposition surfaces. By combining the species mass conservation equations with the electroneutrality constraint, a Poisson equation that explicitly describes the electrolyte potential was derived. The set of coupled, nonlinear equations governing species transport, electric potential, velocity, hydrodynamic pressure, and mesh motion were solved in GOMA, using the finite-element method and a fully-coupled implicit solution scheme via Newton's method. By treating the finite-element mesh as a pseudo solid with an arbitrary Lagrangian-Eulerian formulation and by repeatedly performing re-meshing with CUBIT and re-mapping with MAPVAR, the moving deposition surfaces were tracked explicitly from start of deposition until the trenches were filled with metal, thus enabling the computation of local current densities that potentially influence the microstructure and frictional/mechanical properties of the deposit. The multi-dimensional, multi-species, transient computational framework was demonstrated in case studies of two-dimensional nickel electrodeposition in single and multiple trenches, without and with bath stirring or forced flow. Effects of buoyancy-induced convection on deposition were also investigated. To further illustrate its utility, the framework was employed to simulate deposition in microscreen-based LIGA molds. Lastly, future needs for modeling LIGA electrodeposition are discussed.
One challenge faced by engineers today is replicating an operating environment such as transportation in a test lab. This paper focuses on the process of identifying sine-on-random content in an aircraft transportation environment, although the methodology can be applied to other events. The ultimate goal of this effort was to develop an automated way to identify significant peaks in the PSDs of the operating data, catalog the peaks, and determine whether each peak was sinusoidal or random in nature. This information helps design a test environment that accurately reflects the operating environment. A series of Matlab functions have been developed to achieve this goal with a relatively high degree of accuracy. The software is able to distinguish between sine-on-random and random-on-random peaks in most cases. This paper describes the approach taken for converting the time history segments to the frequency domain, identifying peaks from the resulting PSD, and filtering the time histories to determine the peak amplitude and characteristics. This approach is validated through some contrived data, and then applied to actual test data. Observations and conclusions, including limitations of this process, are also presented.
The experimental and computational investigations of nanosecond electrical explosion of thin Al wire in vacuum are presented. We have demonstrated that increasing the current rate leads to increased energy deposited before voltage collapse. Laser shadowgrams of the overheated Al core exhibit axial stratification with a {approx}100 {micro}m period. The experimental evidence for synchronization of the wire expansion and light emission with voltage collapse is presented. Two-wavelength interferometry shows an expanding Al core in a low-ionized gas condition with increasing ionization toward the periphery. Hydrocarbons are indicated in optical spectra and their influence on breakdown physics is discussed. The radial velocity of low-density plasma reaches a value of {approx}100 km/s. The possibility of an overcritical phase transition due to high pressure is discussed. 1D MHD simulation shows good agreement with experimental data. MHD simulation demonstrates separation of the exploding wire into a high-density cold core and a low-density hot corona as well as fast rejection of the current from the wire core to the corona during voltage collapse. Important features of the dynamics for wire core and corona follow from the MHD simulation and are discussed.
Seeding and autocatalytic reduction of platinum salts in aqueous surfactant solution using ascorbic acid as the reductant leads to remarkable dendritic metal nanostructures. In micellar surfactant solutions, spherical dendritic metal nanostructures are obtained, and the smallest of these nanodendrites resemble assemblies of joined nanoparticles and the nanodendrites are single crystals. With liposomes as the template, dendritic platinum sheets in the form of thin circular disks or solid foam-like nanomaterials can be made. Synthetic control over the morphology of these nanodendrites, nanosheets, and nanostructured foams is realized by using a tin-porphyrin photocatalyst to conveniently and effectively produce a large initial population of catalytic growth centers. The concentration of seed particles determines the ultimate average size and uniformity of these novel two- and three-dimensional platinum nanostructures.
On April 22 and 23, 2004, a diverse group of 14 policymakers, modelers, analysts, and scholars met with some 22 members of the Sandia National Laboratories staff to explores ways in which the relationships between modelers and policymakers in the energy and environment fields (with an emphasis on energy) could be made more productive for both. This report is not a transcription of that workshop, but draws very heavily on its proceedings. It first describes the concept of modeling, the varying ways in which models are used to support policymaking, and the institutional context for those uses. It then proposes that the goal of modelers and policymakers should be a relationship of mutual trust, built on a foundation of communication, supported by the twin pillars of policy relevance and technical credibility. The report suggests 20 guidelines to help modelers improve the relationship, followed by 10 guidelines to help policymakers toward the same goal.
The Vulcan fire-field model is employed to simulate the evolution of pool fires and the distribution of fire suppressants in a engine nacelle simulator. The objective is to identify conditions for which suppression will and will not be successful in order to (1) provide input on experimental design and (2) to test the model's predictive capabilities through comparison with future test results. Pool fires, where the fuel pool is on the bottom of the nacelle, have been selected for these tests because they have been identified as among the most challenging to suppress. Modeling of the production HFC-125 fire suppression system predicts that all pool fires are extinguished. Removing nozzles and reducing the rate of suppressant injection eventually lead to a predicted failure to suppress the fires. The stability of the fires, and therefore the difficulty in extinguishing them, depends on a variety of additional factors as discussed in the text.
This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator capable of simulating electrical circuits at a variety of abstraction levels. Primarily, Xyce has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability the current state-of-the-art in the following areas: {sm_bullet} Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). Note that this includes support for most popular parallel and serial computers. {sm_bullet} Improved performance for all numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. {sm_bullet} Device models which are specifically tailored to meet Sandia's needs, including many radiation-aware devices. {sm_bullet} A client-server or multi-tiered operating model wherein the numerical kernel can operate independently of the graphical user interface (GUI). {sm_bullet} Object-oriented code design and implementation using modern coding practices that ensure that the Xyce Parallel Electronic Simulator will be maintainable and extensible far into the future. Xyce is a parallel code in the most general sense of the phrase - a message passing of computing platforms. These include serial, shared-memory and distributed-memory parallel implementation - which allows it to run efficiently on the widest possible number parallel as well as heterogeneous platforms. Careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. One feature required by designers is the ability to add device models, many specific to the needs of Sandia, to the code. To this end, the device package in the Xyce These input formats include standard analytical models, behavioral models look-up Parallel Electronic Simulator is designed to support a variety of device model inputs. tables, and mesh-level PDE device models. Combined with this flexible interface is an architectural design that greatly simplifies the addition of circuit models. One of the most important feature of Xyce is in providing a platform for computational research and development aimed specifically at the needs of the Laboratory. With Xyce, Sandia now has an 'in-house' capability with which both new electrical (e.g., device model development) and algorithmic (e.g., faster time-integration methods) research and development can be performed. Ultimately, these capabilities are migrated to end users.
This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users' Guide. The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users' Guide.
The surface micromachining processes used to manufacture MEMS devices and integrated circuits transpire at such small length scales and are sufficiently complex that a theoretical analysis of them is particularly inviting. Under development at Sandia National Laboratories (SNL) is Chemically Induced Surface Evolution with Level Sets (ChISELS), a level-set based feature-scale modeler of such processes. The theoretical models used, a description of the software and some example results are presented here. The focus to date has been of low-pressure and plasma enhanced chemical vapor deposition (low-pressure chemical vapor deposition, LPCVD and PECVD) processes. Both are employed in SNLs SUMMiT V technology. Examples of step coverage of SiO{sub 2} into a trench by each of the LPCVD and PECVD process are presented.
The thermochemistry of the transition-metal fluorides and chlorides MF{sub n} and MCl{sub n} (M = Cr, Mn, Fe; n = 1, 2) has been characterized by high-level ab initio electronic structure methods. Geometries and harmonic vibrational frequencies were computed at the B3LYP level of theory using triple-{zeta} basis sets including diffuse and polarization functions. Heats of formation were computed from isogyric reaction energies at the CCSD(T) level using high-quality basis sets, including corrections for core-valence correlation and scalar relativistic effects. To investigate the possible linearity of the ground states of CrCl{sub 2} and CrF{sub 2}, we performed geometry optimizations for these species at the CCSD(T) level using large basis sets. In both cases, a bent ({sup 5}B{sub 2}) minimum structure was located, but the bent structure is only slightly below the linear form, which was found to be a transition state. For all of the investigated halides, polynomial fits were carried out for the heat capacity and the standard enthalpy and entropy in the 300-3000 K temperature range.
The modeling of fluid/structure interaction is of growing importance in both energy and environmental applications. Because of the inherent complexity, these problems must be simulated on parallel machines in order to achieve high resolution. The purpose of this research was to investigate techniques for coupling flow and geomechanics in porous media that are suitable for parallel computation. In particular, our main objective was to develop an iterative technique which can be as accurate as a fully coupled model but which allows for robust and efficient coupling of existing complex models (software). A parallel linear elastic module was developed which was coupled to a three phase three-component black oil model in IPARS (Integrated Parallel Accurate Reservoir Simulator). An iterative de-coupling technique was introduced at each time step. The resulting nonlinear iteration involved solving for displacements and flow sequentially. Rock compressibility was used in the flow model to account for the effect of deformation on the pore volume. Convergence was achieved when the mass balance for each component satisfied a given tolerance. This approach was validated by comparison with a fully coupled approach implemented in the British PetroledAmoco ACRES simulator. Another objective of this work was to develop an efficient parallel solver for the elasticity equations. A preconditioned conjugate gradient solver was implemented to solve the algebraic system arising from tensor product linear Galerkin approximations for the displacements. Three preconditioners were developed: LSOR (line successive over-relaxation), block Jacobi, and agglomeration multi-grid. The latter approach involved coarsening the 3D system to 2D and using LSOR as a smoother that is followed by applying geometric multi-grid with SOR (successive over-relaxation) as a smoother. Preliminary tests on a 64-node Beowulf cluster at CSM indicate that the agglomeration multi-grid approach is robust and efficient.
The couple on a ball rotating relative to an otherwise quiescent suspension of comparably-sized, neutrally buoyant spheres is studied both experimentally and numerically. Apparent 'slip' relative to the analytical solution for a sphere spinning in a Newtonian fluid (based upon the viscosity of the suspension) is determined in suspensions with volume fractions c ranging from 0.03 to 0.50. This apparent slip results in a decrease of the measured torque on the spinning ball when the radius of the ball becomes comparable with that of the suspended spheres. Over the range of our data, the slip becomes more pronounced as the concentration c increases. At c = 0.25, three-dimensional boundary-element simulations agree well with the experimental data. Moreover, at c = 0.03, good agreement exists between such calculations and theoretical predictions of rotary slip in dilute suspensions.
