Publications

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We summarize the results of a project to develop evolutionary computing methods for the design of behaviors of embodied agents in the form of autonomous vehicles. We conceived and implemented a strategy called graduated embodiment. This method allows high-level behavior algorithms to be developed using genetic programming methods in a low-fidelity, disembodied modeling environment for migration to high-fidelity, complex embodied applications. This project applies our methods to the problem domain of robot navigation using adaptive waypoints, which allow navigation behaviors to be ported among autonomous mobile robots with different degrees of embodiment, using incremental adaptation and staged optimization. Our approach to biomimetic behavior engineering is a hybrid of human design and artificial evolution, with the application of evolutionary computing in stages to preserve building blocks and limit search space. The methods and tools developed for this project are directly applicable to other agent-based modeling needs, including climate-related conflict analysis, multiplayer training methods, and market-based hypothesis evaluation.

This report documents the results of an LDRD program entitled 'System of Systems Modeling and Analysis' that was conducted during FY 2003 and FY 2004. Systems that themselves consist of multiple systems (referred to here as System of Systems or SoS) introduce a level of complexity to systems performance analysis and optimization that is not readily addressable by existing capabilities. The objective of the 'System of Systems Modeling and Analysis' project was to develop an integrated modeling and simulation environment that addresses the complex SoS modeling and analysis needs. The approach to meeting this objective involved two key efforts. First, a static analysis approach, called state modeling, has been developed that is useful for analyzing the average performance of systems over defined use conditions. The state modeling capability supports analysis and optimization of multiple systems and multiple performance measures or measures of effectiveness. The second effort involves time simulation which represents every system in the simulation using an encapsulated state model (State Model Object or SMO). The time simulation can analyze any number of systems including cross-platform dependencies and a detailed treatment of the logistics required to support the systems in a defined mission.

Single molecule fluorophores were studied for the first time with a new confocal fluorescence microscope that allows the wavelength and emission time to be simultaneously measured with single molecule sensitivity. In this apparatus, the photons collected from the sample are imaged through a dispersive optical system onto a time and position sensitive detector. This detector records the wavelength and emission time of each detected photon relative to an excitation laser pulse. A histogram of many events for any selected spatial region or time interval can generate a full fluorescence spectrum and correlated decay plot for the given selection. At the single molecule level, this approach makes entirely new types of temporal and spectral correlation spectroscopy of possible. This report presents the results of simultaneous time- and frequency-resolved fluorescence measurements of single rhodamine 6G (R6G), tetramethylrhodamine (TMR), and Cy3 embedded in thin films of polymethylmethacrylate (PMMA).

Radio frequency microelectromechanical systems (RF MEMS) are an enabling technology for next-generation communications and radar systems in both military and commercial sectors. RF MEMS-based reconfigurable circuits outperform solid-state circuits in terms of insertion loss, linearity, and static power consumption and are advantageous in applications where high signal power and nanosecond switching speeds are not required. We have demonstrated a number of RF MEMS switches on high-resistivity silicon (high-R Si) that were fabricated by leveraging the volume manufacturing processes available in the Microelectronics Development Laboratory (MDL), a Class-1, radiation-hardened CMOS manufacturing facility. We describe novel tungsten and aluminum-based processes, and present results of switches developed in each of these processes. Series and shunt ohmic switches and shunt capacitive switches were successfully demonstrated. The implications of fabricating on high-R Si and suggested future directions for developing low-loss RF MEMS-based circuits are also discussed.

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The focus of this paper is a penalty-based strategy for preconditioning elliptic saddle point systems. As the starting point, we consider the regularization approach of Axelsson in which a related linear system, differing only in the (2,2) block of the coefficient matrix, is introduced. By choosing this block to be negative definite, the dual unknowns of the related system can be eliminated resulting in a positive definite primal Schur complement. Rather than solving the Schur complement system exactly, an approximate solution is obtained using a substructuring preconditioner. The approximate primal solution together with the recovered dual solution then define the preconditioned residual for the original system. The approach can be applied to a variety of different saddle point problems. Although the preconditioner itself is symmetric and indefinite, all the eigenvalues of the preconditioned system are real and positive if certain conditions hold. Stronger conditions also ensure that the eigenvalues are bounded independently of mesh parameters. An interesting feature of the approach is that conjugate gradients can be used as the iterative solution method rather than GMRES. The effectiveness of the overall strategy hinges on the preconditioner for the primal Schur complement. Interestingly, the primary condition ensuring real and positive eigenvalues is satisfied automatically in certain instances if a Balancing Domain Decomposition by Constraints (BDDC) preconditioner is used. Following an overview of BDDC, we show how its constraints can be chosen to ensure insensitivity to parameter choices in the (2,2) block for problems with a divergence constraint. Examples for different saddle point problems are presented and comparisons made with other approaches.

Confinement within the nanoscale pores of a zeolite strongly modifies the behavior of small molecules. Typical of many such interesting and important problems, realistic modeling of this phenomena requires simultaneously capturing the detailed behavior of chemical bonds and the possibility of collective dynamics occurring in a complex unit cell (672 atoms in the case of Zeolite-4A). Classical simulations alone cannot reliably model the breaking and formation of chemical bonds, while quantum methods alone are incapable of treating the extended length and time scales characteristic of complex dynamics. We have developed a robust and efficient model in which a small region treated with the Kohn-Sham density functional theory is embedded within a larger system represented with classical potentials. This model has been applied in concert with first-principles electronic structure calculations and classical molecular dynamics and Monte Carlo simulations to study the behavior of water, ammonia, the hydroxide ion, and the ammonium ion in Zeolite-4a. Understanding this behavior is important to the predictive modeling of the aging of Zeolite-based desiccants. In particular, we have studied the absorption of these molecules, interactions between water and the ammonium ion, and reactions between the hydroxide ion and the zeolite cage. We have shown that interactions with the extended Zeolite cage strongly modifies these local chemical phenomena, and thereby we have proven out hypothesis that capturing both local chemistry and collective phenomena is essential to realistic modeling of this system. Based on our results, we have been able to identify two possible mechanisms for the aging of Zeolite-based desiccants.

Laser diode ignition experiments were conducted in an effort to characterize the effects of scale and heating rate on micro-scale explosive ignition criteria. Over forty experiments were conducted with various laser power densities and laser spot sizes. In addition, relatively simple analytical and numerical calculations were performed to assist with interpretation of the experimental data and characterization of the explosive ignition criteria.

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A series of numerical simulations have been performed to determine scaling laws for fast ignition break even of a hot spot formed by energetic particles created by a short pulse laser. Hot spot break even is defined to be when the fusion yield is equal to the total energy deposited in the hot spot through both the initial compression and the subsequent heating. In these simulations, only a small portion of a previously compressed mass of deuterium-tritium fuel is heated on a short time scale, i.e., the hot spot is tamped by the cold dense fuel which surrounds it. The hot spot tamping reduces the minimum energy required to obtain break even as compared to the situation where the entire fuel mass is heated, as was assumed in a previous study [S. A. Slutz, R. A. Vesey, I. Shoemaker, T. A. Mehlhorn, and K. Cochrane, Phys. Plasmas 7, 3483 (2004)]. The minimum energy required to obtain hot spot break even is given approximately by the scaling law E{sub T} = 7.5({rho}/100){sup -1.87} kJ for tamped hot spots, as compared to the previously reported scaling of E{sub UT} = 15.3({rho}/100){sup -1.5} kJ for untamped hotspots. The size of the compressed fuel mass and the focusability of the particles generated by the short pulse laser determines which scaling law to use for an experiment designed to achieve hot spot break even.

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This article provides a brief review of the field of electroporation and introduces a new microdevice that facilitates studies to test theories, gain understanding, and control this important biomedical technology. Electroporation, a bio-electrochemical process whose fundamentals are not yet understood, is a means of permeating the cell membrane by applying a voltage across the cell and forming nano-scale pores in the membrane. It has become an important field in biotechnology and medicine for the controlled introduction of macromolecules, such as gene constructs and drugs, into various cells. It is viewed as an engineering alternative to biological techniques for the genetic engineering of cells. To study and control electroporation, we have created a low-cost microelectroporation chip that incorporates a live biological cell with an electric circuit. The device revealed an important behavior of cells in electrical fields. They produce measurable electrical information about the electroporation state of the cell that may enable precise control of the process. The device can be used to facilitate fundamental studies of electroporation and can become useful in providing precise control over biotechnological processes.

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This document provides a detailed discussion and a guide for the use of the RadCat 2.0 Graphical User Interface input file generator for the RADTRAN 5.5 code. The differences between RadCat 2.0 and RadCat 1.0 can be attributed to the differences between RADTRAN 5 and RADTRAN 5.5 as well as clarification for some of the input parameters. 3

The synthesis of a photoswitchable polymer by grafting an azobenzene dye to methacrylate followed by polymerization is presented. The azobenzene dye undergoes a trans-cis photoisomerization that causes a persistent change in the refractive index of cast polymer films. This novel polymer was incorporated into superlattices prepared by spin casting and the optical activity of the polymer was maintained. A modified coextruder that allows the rapid production of soft matter superlattices was designed and fabricated.

Two methods for creating a hybrid level-set (LS)/particle method for modeling surface evolution during feature-scale etching and deposition processes are developed and tested. The first method supplements the LS method by introducing Lagrangian marker points in regions of high curvature. Once both the particle set and the LS function are advanced in time, minimization of certain objective functions adjusts the LS function so that its zero contour is in closer alignment with the particle locations. It was found that the objective-minimization problem was unexpectedly difficult to solve, and even when a solution could be found, the acquisition of it proved more costly than simply expanding the basis set of the LS function. The second method explored is a novel explicit marker-particle method that we have named the grid point particle (GPP) approach. Although not a LS method, the GPP approach has strong procedural similarities to certain aspects of the LS approach. A key aspect of the method is a surface rediscretization procedure--applied at each time step and based on a global background mesh--that maintains a representation of the surface while naturally adding and subtracting surface discretization points as the surface evolves in time. This method was coded in 2-D, and tested on a variety of surface evolution problems by using it in the ChISELS computer code. Results shown for 2-D problems illustrate the effectiveness of the method and highlight some notable advantages in accuracy over the LS method. Generalizing the method to 3D is discussed but not implemented.

Understanding and characterizing the electrical properties of multi-conductor shielded and unshielded cables is an important endeavor for many diverse applications, including airlines, land based communications, nuclear weapons, and any piece of hardware containing multi-conductor cabling. Determining the per unit length capacitance and inductance based on the geometry of the conductors, number of conductors, and characteristics of the shield can prove quite difficult. Relating the inductance and capacitance to shielding effectiveness can be even more difficult. An exceedingly large number of measurements were taken to characterize eight multi-conductor cables, of which four were 3-conductor cables and four were 18-conductor cables. Each set of four cables contained a shielded cable and an unshielded cable with the inner conductors twisted together and a shielded cable and an unshielded cable with the inner conductors not twisted together (or straight). Male LJT connectors were attached on either end of the cable and each cable had a finished length of 22.5 inches. The measurements performed were self and mutual inductance, self and mutual capacitance, and effective height. For the 18 conductor case there ended up being an 18 by 18 element matrix for inductance (with the self inductance terms lying on the diagonal) and an 18 by 18 matrix for capacitance. The effective height of each cable was measured over a frequency range from 220 MHz to 18 GHz in a Mode-Stirred Chamber. The effective height of each conductor of each cable was measured individually and all shorted together, producing 19 frequency responses for each 18 conductor cable. Shielding effectiveness was calculated using the effective heights from the shielded and unshielded cables. The results of these measurements and the statistical analysis of the data will be presented. There will also be a brief presentation of comparison with numerical models.

This report describes an approach for extending the one-dimensional turbulence (ODT) model of Kerstein [6] to treat turbulent flow in three-dimensional (3D) domains. This model, here called ODTLES, can also be viewed as a new LES model. In ODTLES, 3D aspects of the flow are captured by embedding three, mutually orthogonal, one-dimensional ODT domain arrays within a coarser 3D mesh. The ODTLES model is obtained by developing a consistent approach for dynamically coupling the different ODT line sets to each other and to the large scale processes that are resolved on the 3D mesh. The model is implemented computationally and its performance is tested and evaluated by performing simulations of decaying isotropic turbulence, a standard turbulent flow benchmarking problem.

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Military test and training ranges operate with live fire engagements to provide realism important to the maintenance of key tactical skills. Ordnance detonations during these operations typically produce minute residues of parent explosive chemical compounds. Occasional low order detonations also disperse solid phase energetic material onto the surface soil. These detonation remnants are implicated in chemical contamination impacts to groundwater on a limited set of ranges where environmental characterization projects have occurred. Key questions arise regarding how these residues and the environmental conditions (e.g., weather and geostratigraphy) contribute to groundwater pollution impacts. This report documents interim results of a mass transfer model evaluating mass transfer processes from solid phase energetics to soil pore water based on experimental work obtained earlier in this project. This mass transfer numerical model has been incorporated into the porous media simulation code T2TNT. Next year, the energetic material mass transfer model will be developed further using additional experimental data.

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