This paper describes a genetic algorithm application to the DNA fragment assembly problems. The genetic algorithm uses a random key representation for representing the orderings of fragments. Two different fitness functions, both based on pairwise overlap strengths between fragments, were tested. The paper concludes that the genetic algorithm is a promising method for fragment assembly problems, achieving usable solutions quickly, but that the current fitness functions are flawed and that other representations might be more appropriate.

This paper describes a genetic algorithm application to the DNA fragment assembly problems. The genetic algorithm uses a random key representation for representing the orderings of fragments. Two different fitness functions, both based on pairwise overlap strengths between fragments, were tested. The paper concludes that the genetic algorithm is a promising method for fragment assembly problems, achieving usable solutions quickly, but that the current fitness functions are flawed and that other representations might be more appropriate.

A detailed chemical kinetic reaction mechanism is used to study the oxidation of n-heptane under several classes of conditions. Experimental results from ignition behind reflected shock waves and in a rapid compression machine were used to develop and validate the reaction mechanism at relatively high temperatures, while data from a continuously stirred tank reactor (cstr) were used to refine the low temperature portions of the reaction mechanism. In addition to the detailed kinetic modeling, a global or lumped kinetic mechanism was used to study the same experimental results. The lumped model was able to identify key reactions and reaction paths that were most sensitive in each experimental regime and provide important guidance for the detailed modeling effort. In each set of experiments, a region of negative temperature coefficient (NTC) was observed. Variation in pressure from 5 to 40 bars were found to change the temperature range over which the NTC region occurred. Both the lumped and detailed kinetic models reproduced the measured results in each type of experiments, including the features of the NTC region, and the specific elementary reactions and reaction paths responsible for this behavior were identified and rate expressions for these reactions were determined.

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The performance requirements of the Advanced Photon Source (APS) challenge the control system in a number of areas. This paper will review a few applications of advanced technology in the control and monitoring of the APS. The application of digital signal processors (DSPs) and techniques will be discussed, both from the perspective of a large distributed multiprocessor system and from that of embedded systems. In particular, two embedded applications will be highlighted, a beam position monitor processor and a DSP-based power supply controller. Fast data distribution is often a requirement. The application of a high-speed network based on reflective memory will also be discussed in the context of the APS global orbit feedback system. Timing systems provide opportunities to apply technologies such as high-speed logic and fiber optics. Examples of the use of these technologies will also be included. Finally, every modern accelerator control system of any size requires networking. Features of the APS accelerator controls network will be discussed.

An alternative to using a large graphical display manager like MEDM [1,2] to interface to a control system, is to use individual control objects, such as text boxes, meters, etc., running in a browser. This paper presents three implementations of this concept, one using ActiveX controls, one with Java applets, and another with Microsoft Agent. The ActiveX controls have performance nearing that of MEDM, but they only work on Windows platforms. The Java applets require a server to get around Web security restrictions and are not as fast, but they have the advantage of working on most platforms and with both of the leading Web browsers. The agent works on Windows platforms with and without a browser and allows voice recognition and speech synthesis, making it somewhat more innovative than MEDM.

The primary reference fuels n-heptane and iso-octane and their mixtures are used as a measure of the tendency of a given automotive fuel to cause knocking or pre-ignition in an internal combustion engine. Consequently, many experimental studies have been performed on these hydrocarbons in an attempt to better understand their oxidation. Shock tube studies at high temperature and pressure have been performed. Low temperature studies, in which species concentration profiles of primary, intermediate and final products, have been carried out using jet stirred flow reactors. In addition, experiments have been performed in CFR engines and fundamental features of n-heptane autoignition have been observed using a rapid compression machine. A detailed chemical kinetic reaction mechanism is employed here to study the oxidation of both fuels. Computed results are compared with experimental data obtained in the High Pressure Turbulent Flow Reactor at Princeton University.

The effect of possible accidental beam loss in LHC on the IP5 insertion elements and CMS detector is studied via realistic Monte Carlo simulations. Such beam loss could be the consequence of an unsynchronized abort or � in worst case � an accidental prefire of one of the abort kicker modules. Simulations with the STRUCT code show that this beam losses would take place in the IP5 inner and outer triplets. MARS simulations of the hadronic and electro-magnetic cascades induced in such an event indicate severe heating of the inner triplet quadrupoles. In order to protect the IP5 elements, two methods are proposed: a set of shadow collimators in the outer triplet and a prefired module compensation using a special module charged with an opposite voltage (antikicker). The remnants of the accidental beam loss entering the experimental hall have been used as input for FLUKA simulations in the CMS detector. It is shown that it is vital to take measures to reliably protect the expensive CMS tracker components.

Piezoresistive stress sensing chips have been used extensively for measurement of assembly related die surface stresses. Although many experiments can be performed with resistive structures which are directly bonded, for extensive stress mapping it is necessary to have a large number of sensor cells which can be addressed using CMOS logic circuitry. Our previous test chip, the ATC04, has 100 cells, each approximately 0.012 in. on a side, on a chip with a side dimension of 0.45 in. When a cell resistor is addressed, it is connected to a four terminal measurement bus through CMOS transmission gates. In theory, the gate resistances do not affect the measurement. In practice, there may be subtle effects which appear when very high accuracy is required. At high temperatures, gate leakage can increase to a point at which the resistor measurement becomes inaccurate. For ATC04 this occurred at or above 50 C. Here, we report on the first measurements obtained with a new prototype test chip, the ATC06. This prototype was fabricated in a 0.5 micron feature size silicided CMOS process using the MOSIS prototyping facility. The cell size was approximately 0.004 in. on a side. In order to achieve piezoresistive behavior for the …

An integrated computational tool named the Production Planning Model (ProdMod) has been developed to simulate the operation of the entire high level waste complex (HLW) at the Savannah River Site (SRS) over its full life cycle. ProdMod is used to guide SRS management in operating the waste complex in an economically efficient and environmentally sound manner. SRS HLW operations are modeled using coupled algebraic equations. The dynamic nature of plant processes is modeled in the form of a linear construct in which the time dependence is implicit. Batch processes are modeled in discrete event-space, while continuous processes are modeled in time-space. The ProdMod methodology maps between event-space and time-space such that the inherent mathematical discontinuities in batch process simulation are avoided, without sacrificing any of the necessary detail in the batch recipe steps. Modeling the processes separately in event- and time-space using linear constructs, and then coupling the two spaces, has accelerated the speed of simulation compared to a typical dynamic simulation. The ProdMod simulator models have been validated against operating data and other computer codes. Case studies have demonstrated the usefulness of the ProdMod simulator in developing strategies that demonstrate significant cost savings in operating the SRS HLW complex …

CDF searches for R{sub p} violation, extra quark generations, and long-lived charged massive particles are presented. These phenomena are not predicted by the Minimal Supersymmetric Standard Model (MSSM) and therefore complement the classic SUSY searches. Prospects for continuing these analyses during Run II of the Tevatron are outlined.

Based on realistic Monte-Carlo simulations a two-stage beam collimation system is designed to minimize the beam loss in the Fermilab Tevatron for fixed target and collider Run II. Thin primary collimators are used to increase particle amplitude and their impact parameter on the down-stream secondary collimators. This results in a significant reduction of the total beam loss in the machine, decreases collimator overheating and mitigates requirements to colli-mator alignment. A set of collimators will originally be in-stalled for fixed target operation and for antiprotonbeam re-cycling studies. The collimation system improvement will continue into the collider Run II and intensity upgrade.

This article presents recent results of searches for Supersymmetry using the CDF and the DO detector at the Fermilab Tevatron Collider. Described are the Tevatron searches for third generation scalar quarks and for supersymmetric signatures involving photons. All the reported results have been obtained assuming theoretical models in which R-parity is conserved.

A table top servohydraulic load frame equipped with a laser displacement measurement system was constructed for the mechanical characterization of LIGA fabricated electroforms. A drop in tensile specimen geometry which includes a pattern to identify gauge length via laser scanning has proven to provide a convenient means to monitor and characterize mechanical property variations arising during processing. In addition to tensile properties, hardness and metallurgical data were obtained for nickel deposit specimens of current density varying between 20 and 80 mA/cm{sup 2} from a sulfamate based bath. Data from 80/20 nickel-iron deposits is also presented for comparison. As expected, substantial mechanical property differences from bulk metal properties are observed as well as a dependence of material strength on current density which is supported by grain size variation. While elastic modulus values of the nickel electrodeposit are near 160 GPa, yield stress values vary by over 60%. A strong orientation in the metal electrodeposits as well as variations in nucleating and growth morphology present a concern for anisotropic and geometry dependent mechanical properties within and between different LIGA components.

Recent K-shell scaling experiments on the 20 MA Z accelerator at Sandia National Laboratories have shown that large diameter (40 and 55 mm) arrays can be imploded with 80 to 210 wires of titanium or stainless steel. These implosions have produced up to 150 kJ of > 4.5 keV x-rays and 65 kJ of > 6.0 keV x-rays in 7 to 18 ns FWHM pulses. This is a major advance in plasma radiation source (PRS) capability since there is presently limited test capability above 3 keV. In fact, Z produces more > 4.5 keV x-rays than previous aboveground simulators produced at 1.5 keV. Z also produces some 200 kJ of x-rays between 1 and 3 keV in a continuous spectrum for these loads. The measured spectra and yields are consistent with 1-dimensional MHD calculations performed by NRL. Thermoelastic calorimeters, PVDF gauges, and optical impulse gauges have been successfully fielded with these sources.

MEDM, which is derived from Motif Editor and Display Manager, is the primary graphical interface to the EPICS control system. This paper describes new features that have been added to MEDM in the last two years. These features include new editing capabilities, a PV Info dialog box, a means of specifying limits and precision, a new implementation of the Cartesian Plot, new features for several objects, new capability for the Related Display, help, a user-configurable Execute Menu, reconfigured start-up options, and availability for Windows 95/98/NT. Over one hundred bugs have been fixed, and the program is quite stable and in extensive use.

During the qualification of a new high reliability low-temperature cofired ceramic (LTCC) multichip module (MCM), two issues relating to the electrical and mechanical integrity of the LTCC network were encountered while performing qualification testing. One was electrical opens after aging tests that were caused by cracks in the solder joints. The other was fracturing of the LTCC networks during mechanical testing. Through failure analysis, computer modeling, bend testing, and test samples, changes were identified. Upon implementation of all these changes, the modules passed testing, and the MCM was placed into production.

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The paper describes a laboratory safety benchmarking initiative conducted by Lawrence Livermore National Laboratory. Several private and government research laboratories were assessed with respect to their safety systems, management controls, and employee involvement. The laboratories with the best safety records were compared to those with average to poor safety histories.

A gate-turn-off (GTO) switch is under development at the Advanced Photon Source as a replacement for a thyratron switch in high power pulsed application. The high voltage in the application requires multiple GTOs connected in series. One component that is critical to the success of GTO operation is the gate drive circuit. The gate drive circuit has to provide fast high-current pulses to the GTO gate for fast turn-on and turn-off. It also has to be able to operate while floating at high voltage. This paper describes a gate drive circuit that meets these requirements.

An analog rf gap voltage regulation system has been designed and built at Argonne National Laboratory to maintain constant total storage ring rf gap voltage, independent of beam loading and cavity tuning effects. The design uses feedback control of the klystron mod-anode voltage to vary the amount of rf power fed to the storage ring cavities. The system consists of two independent feedback loops, each regulating the combined rf gap voltages of eight storage ring cavities by varying the output power of either one or two rf stations, depending on the mode of operation. It provides full operator control and permissive logic to permit feedback control of the rf system output power only if proper conditions are met. The feedback system uses envelope-detected cavity field probe outputs as the feedback signal. Two different methods of combining the individual field probe signals were used to generate a relative DC level representing one-half of the total storage ring rf voltage, an envelope-detected vector sum of the field probe rf signals, and the DC sum of individual field probe envelope detector outputs. The merits of both methods are discussed. The klystron high-voltage power supply (HVPS) units are fitted with an analog interface for …

Magnet errors and off-center orbits through sextuples perturb the dispersion and beta functions in a storage ring (SR), which affects machine performance. In a large ring such as the Advanced Photon Source (APS), the magnet errors are difficult to determine with beam-based methods. Also the non-zero orbit through sextuples result from user requests for steering at light source points. For expediency, a singular value decomposition (SVD) matrix method analogous to orbit correction was adopted to make global corrections to these functions using strengths of several quadrupoles as correcting elements. The direct response matrix is calculated from the model of the perfect lattice. The inverse is calculated by SVD with a selected number of singular vectors. Resulting improvement in the lattice functions and machine performance will be presented.

Lawrence Livermore National Laboratory (LLNL)l is developing a prototype imaging radar for inspecting steel reinforced concrete bridge decks. The system is designed to acquire Synthetic Aperture Radar (SAR) data and provide high-resolution images of internal structure, flaws, and defects enabling bridge inspectors to nondestructively evaluate and characterize bridge deck condition. Concrete delamination resulting from corrosion of steel reinforcing bars (rebars) is an important structural defect that the system is designed to detect. The prototype system uses arrays of compact, low-cost Micropower Impulse Radar (MIR) modules, supported by appropriate data acquisition and storage subsystems, to generate and collect the radar data, and unique imaging codes to reconstruct images of bridge deck internals. In this paper, we provide an overview of the prototype system concept, discuss its expected performance, and present recent experimental results showing the capability of this approach to detect thin delamination simulations embedded in concrete.

Last year a second-generation SSRL-type thermionic cathode rf gun was installed in the Advanced Photon Source (APS) linac. This gun (referred to as ''gun2'') has been successfully commissioned and now serves as the main injector for the APS linac, essentially replacing the Koontz-type DC gun. To help ensure injector availability, particularly with the advent of top-up mode operation at the APS, a second thermionic-cathode rf gun will be installed in the APS linac to act as a hot-spare beam source. The hot-spare installation includes several unique design features, including a deep-orbit Panofsky-style alpha magnet. Details of the hot-spare beamline design and projected performance are presented, along with some plans for future performance upgrades.