William Sandberg

Computation of the 3-D Unsteady Flow Past Deforming Geometries

A 3-D incompressible unsteady flow solver based on simple finite elements with adaptive remeshing and grid movement for both moving and deforming surfaces is described. We demonstrate the combination of adaptive remeshing techniques with the incompressible flow solver with the computation of flow past an eel in 2-D and a blue-fin tuna in 3-D. The flow past a swimming tuna was computed for two extreme cases of the caudal fin frequency and swimming speed. A grid refinement study was performed and a grid converged solution for the force produced by the caudal fin was obtained.

Design of a Biomimetic Controlled-Curvature Robotic Pectoral Fin

This paper describes the design, construction, and testing of a biomimetic pectoral (side) fin with actively controlled curvature for UUV propulsion. First, a 3D unsteady computational fluid dynamics (CFD) analysis tool has been adapted to computationally optimize any fin design, followed by a full parametric study based on our findings. Second, this said fin has been constructed, and our working optimized mechanical design is offered. Lastly, we make an experimental vs. computational result comparison for thrust, lift, and flapping moment data - showing that a UUV with this technology can have dramatic improvements in low-speed propulsion and control over traditional thruster methods.

Surface triangulation over intersecting geometries

A method for the rapid construction of meshes over intersecting triangulated shapes is described. The method is based on an algorithm that automatically generates a surface mesh from intersecting triangulated surfaces by means of Boolean intersection/union operations. After the intersection of individual components is obtained, the exposed surface parts are extracted. The algorithm is intended for rapid interactive construction of non-trivial surfaces in engineering design, manufacturing, visualization and molecular modelling applications. Techniques to make the method fast and general are described. The proposed algorithm is demonstrated on a number of examples, including intersections of multiple spheres, planes and general engineering shapes, as well as generation of surface and volume meshes around clusters of intersecting components followed by the computation of flow field parameters. Copyright

Virtual workbench - a non-immersive virtual environment for visualizing and interacting with 3D objects for scientific visualization

The Virtual Workbench (VW) is a non-immersive virtual environment that allows users to view and interact with stereoscopic objects displayed on a workspace similar to a tabletop workspace used in day-to-day life. A VW is an ideal environment for collaborative work where several colleagues can gather around the table to study 3D virtual objects. The Virtual Reality laboratory at the Naval Research Laboratory has implemented the VW using a concept similar to (Froehlich et al., 1994). This paper investigates how the VW can be used as a non-immersive display device for understanding and interpreting complex objects encountered in the scientific visualization field. Different techniques for interacting with 3D visualization objects on the table and using VW as a display device for visualization are evaluated using several cases.

Non-equilibrium all-atom molecular dynamics simulations of free and tethered DNA molecules in nanochannel shear flows

In order to gain insight into the mechanical and dynamical behaviour of free and tethered short chains of ss/ds DNA molecules in flow, and in parallel to investigate the properties of long chain molecules in flow fields, we have developed a series of quantum and molecular methods to extend the well developed equilibrium software CHARMM to handle non-equilibrium dynamics. These methods have been applied to cases of DNA molecules in shear flows in nanochannels. Biomolecules, both free and wall-tethered, have been simulated in the all-atom style in solvent-filled nanochannels. The new methods were demonstrated by carrying out NEMD simulations of free single-stranded DNA (ssDNA) molecules of 21 bases as well as double-stranded DNA (dsDNA) molecules of 21 base pairs tethered on gold surfaces in an ionic water shear flow. The tethering of the linker molecule (6-mercapto-1-hexanol) to perfect Au(111) surfaces was parametrized based on density functional theory (DFT) calculations. Force field parameters were incorporated into the CHARMM database. Gold surfaces are simulated in a Lennard-Jones style model that was fitted to the Morse potential model of bulk gold. The bonding force of attachment of the DNA molecules to the gold substrate linker molecule was computed to be up to a few nN when the DNA molecules are fully stretched at high shear rates. For the first time, we calculated the relaxation time of DNA molecules in picoseconds (ps) and the hydrodynamic force up to a few nanoNewtons (nN) per base pair in a nanochannel flow. The velocity profiles in the solvent due to the presence of the tethered DNA molecules were found to be nonlinear only at high shear flow rates. Free ssDNA molecules in a shear flow were observed to behave differently from each other depending upon their initial orientation in the flow field. Both free and tethered DNA molecules are clearly observed to be stretching, rotating and relaxing. Methods developed in this initial work can be incorporated into multiscale simulations including quantum mechanical, molecular and the microfluidic continuum regimes. The results may also be useful in extending existing macroscopic empirical models of DNA response dynamics in shear flows.

Fuzzy logic PID based control design and performance for a pectoral fin propelled unmanned underwater vehicle

This paper describes the modeling, simulation, and control of a UUV in six degree-of-freedom (6-DOF) motion using two NRL actively controlled-curvature fins. Computational fluid dynamic (CFD) analysis and experimental results are used in modeling the fin as part of the 6-DOF vehicle model. A fuzzy logic proportional-integral-derivative (PID) based control system has been developed to smoothly transition between preprogrammed sets of fin kinematics in order to create a stable and highly maneuverable UUV. Two different approaches to a fuzzy logic PID controller are analyzed: weighted gait combination (WGC), and modification of mean bulk angle bias (MBAB). Advantages and disadvantages of both methods at the vehicle level are discussed. Simulation results show desirable system performance over a wide range of maneuvers.

Density functional study of a typical thiol tethered on a gold surface : ruptures under normal or parallel stretch

The mechanical and dynamical properties of a model Au(111)/thiol surface system were investigated by using localized atomic-type orbital density functional theory in the local density approximation. Relaxing the system gives a configuration where the sulfur atom forms covalent bonds to two adjacent gold atoms as the lowest energy structure. Investigations based on ab initio molecular dynamics simulations at 300, 350 and 370 K show that this tethering system is stable. The rupture behaviour between the thiol and the surface was studied by displacing the free end of the thiol. Calculated energy profiles show a process of multiple successive ruptures that account for experimental observations. The process features successive ruptures of the two Au–S bonds followed by the extraction of one S-bonded Au atom from the surface. The force required to rupture the thiol from the surface was found to be dependent on the direction in which the thiol was displaced, with values comparable with AFM measurements. These results aid the understanding of failure dynamics of Au(111)-thiol-tethered biosurfaces in microfluidic devices where fluidic shear and normal forces are of concern.

Design, Development, and Testing of Flapping Fins with Actively Controlled Curvature for an Unmanned Underwater Vehicle

This paper describes the design, construction, and testing of a biomimetic pectoral (side) fin with actively controlled curvature for UUV propulsion. It also describes the development of a test UUV and the design of a fin control system for vertical plane motion. A 3D unsteady computational fluid dynamics (CFD) analysis has been carried out to computationally optimize the fin design including a full study of the primary design parameters. The fin has been constructed and it can reproduce any specified deformation time-history. The full dynamics of the proposed vehicle have been modeled and the forces produced by the flapping fins computed. Finally, the stability of motion in the vertical plane has been analyzed and a control system has been designed.

3-D Unsteady Computations of Flapping Flight in Insects, Fish, and Unmanned Vehicles

3-D unsteady computations have been carried out for a swimming tuna with an oscillating caudal fin, the flapping flight of the fruit fly and a pectoral fin swimmer, the bird wrasse, and a variety of unmanned air vehicles. Such computations for creatures or vehicles with moving and deforming surfaces can provide information on the dynamics of force production that is quite useful for vehicle design. Novel biomimetic vehicles have been designed and built and their performance is described. As vehicle size decreases there has also been a need for incorporation of novel materials, sensors, and control systems. Computational challenges for coupling novel sensor designs, vehicle timevarying force and moment computations, and self-consistent vehicle trajectory computations are discussed.

Visualization of Shear-Induced Ordering in Atomic Liquids

Abstract A visualizaton and animation capability has been extended to provide insights into the short time dynamics in atomic liquids. Non-Equilibrium Molecular Dynamics shear flow simulations have been carried out in several isotopically substituted Lennard-Jones liquids for four shear rates. The results of these simulations have been visualized and animated to show the computed trajectories of selected atoms and the variation in their local environment in a sheared systems. Linear ordering along the direction of shear is seen at the highest shear rate. This ordered structure is inclined in the plane normal to the shear direction. The local environments about chosen atoms are observed to undergo extensive deviation from a spherical shape.