Boschitsch A.H.,Continuum Dynamics, Inc. |
Fenley M.O.,Florida State University
Journal of Chemical Theory and Computation
An adaptive Cartesian grid (ACG) concept is presented for the fast and robust numerical solution of the 3D Poisson-Boltzmann equation (PBE) governing the electrostatic interactions of large-scale biomolecules and highly charged biomolecular assemblies such as ribosomes and viruses. The ACG offers numerous advantages over competing grid topologies such as regular 3D lattices and unstructured grids. For very large biological molecules and their assemblies, the total number of grid points is several orders of magnitude less than that required in a conventional lattice grid used in the current PBE solvers, thus allowing the end user to obtain accurate and stable nonlinear PBE solutions on a desktop computer. Compared to tetrahedral-based unstructured grids, ACG offers a simpler hierarchical grid structure, which is naturally suited to multigrid, relieves indirect addressing requirements, and uses fewer neighboring nodes in the finite difference stencils. Construction of the ACG and determination of the dielectric/ionic maps are straightforward and fast and require minimal user intervention. Charge singularities are eliminated by reformulating the problem to produce the reaction field potential in the molecular interior and the total electrostatic potential in the exterior ionic solvent region. This approach minimizes grid dependency and alleviates the need for fine grid spacing near atomic charge sites. The technical portion of this paper contains three parts. First, the ACG and its construction for general biomolecular geometries are described. Next, a discrete approximation to the PBE upon this mesh is derived. Finally, the overall solution procedure and multigrid implementation are summarized. Results obtained with the ACG-based PBE solver are presented for (i) a low dielectric spherical cavity, containing interior point charges, embedded in a high dielectric ionic solvent-analytical solutions are available for this case, thus allowing rigorous assessment of the solution accuracy; (ii) a pair of low dielectric charged spheres embedded in an ionic solvent to compute electrostatic interaction free energies as a function of the distance between sphere centers; (iii) surface potentials of proteins, nucleic acids, and their larger-scale assemblies such as ribosomes; and (iv) electrostatic solvation free energies and their salt sensitivities-obtained with both linear and nonlinear Poisson-Boltzmann equations-for a large set of proteins. These latter results along with timings can serve as benchmarks for comparing the performance of different PBE solvers. © 2011 American Chemical Society. Source
Agency: Department of Defense | Branch: Air Force | Program: STTR | Phase: Phase I | Award Amount: 149.89K | Year: 2015
ABSTRACT: Accurate aeroelastic predictions are critical to the development of aircraft and assessment of aircraft/store compatibility since structural deformation and aeroelastic instabilities during flight affect pilot/aircraft safety and mission success. Indeed, several fighter aircraft have demonstrated recurring susceptibility to Limit Cycle Oscillations (LCO) when certain external stores are installed on the aircraft. Despite this critically important issue, the ability to rapidly and accurately predict flutter and LCO with current numerical methods is limited due to modeling fidelity and computational cost. The proposed effort seeks to address these limitations by developing an innovative rapid non-linear physics based flutter/LCO analysis system for implementation on workstation-class hardware. This effort will build upon the extensive experience of Continuum Dynamics, Inc. and Duke University in developing coupled aeromechanics analysis of a wide variety of configurations to bridge the gap between the reduced fidelity models most often used by industry and the resource intensive CFD-based approaches employed in the research environment. The proposed analysis system will be based around a unique variable fidelity non-linear CFD method combined with an innovative analysis procedure and integrated structural dynamics analysis to dramatically reduce the time required to investigate to aeroelastic performance of a new airframe or and store configurations. BENEFIT: A successful SBIR effort would produce an accurate and efficient aeroelastic analysis system for rapidly evaluating airframe and aircraft/store combination stability. This analysis system would directly support the USAFs long-term flutter and LCO prediction goals, particularly with regards to the evaluation of new aircraft/store combinations, aircraft/store modernization efforts and supporting flight test activities. Significant commercialization opportunities are anticipated from licensing the new analysis to major air-vehicle manufacturers and other branches of the government involved in air platform performance enhancement and external stores compatibility.
Agency: Department of Defense | Branch: Army | Program: SBIR | Phase: Phase I | Award Amount: 99.98K | Year: 2015
Accurate full vehicle performance prediction is essential for designing rotorcraft and supporting flight operations. The computational cost of contemporary CFD methods is hampered by excessive numerical dissipation of vorticity, and common methods fail to predict adequately the unsteady rotor and fuselage loading when engineering/design level grids are employed. Continuum Dynamics, Inc. (CDI), Georgia Institute of Technology (GT), and Sikorsky Aircraft Corporation, propose to directly address these limitations while simultaneously supporting ongoing and future Army rotorcraft development and support efforts by developing a suite of variable-fidelity wake prediction methods for improving CFD and enabling breakthrough full rotorcraft interactional aerodynamics modeling capabilities. The proposed approach builds upon work at CDI and GT in CFD, free-wake and hybrid analyses to dramatically reduce the computational cost of complete rotorcraft CFD by developing a robust and efficient overset coupling between DoD CFD/CSD methods and variants of CDIs CHARM and VorTran-M2 solvers that is transparent to the end user. Phase I will see the proof-of-concept development and validation of such an approach, including capabilities assessment and demonstration in a real-world design environment.
Agency: Department of Energy | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 149.93K | Year: 2015
The economic viability of wind energy is critically dependent upon robust, long-duration operation, while minimizing outages and costs for repair and ongoing maintenance. Active load mitigation offers a way to control fatigue-inducing loads so as to forestall major failures, preclude costly repairs and service interruptions, and extend the life of wind turbine blades, generator components and the entire turbine system. Mitigation of loads requires some form of adaptation of the turbine to variable conditions e.g., atmospheric turbulence, wind speed variation, turbine to turbine interaction, tower shadow), and these needs can be addressed through an application of smart materials-based devices to provide on-blade aerodynamic control. Use of low profile control surfaces actuated via Shape Memory Alloy SMA) mechanisms would allow localized aerodynamic load inputs from a simple, robust and cost-effective modification, thereby allowing the direct control of impulsive and fatigue life-limiting oscillatory loads. The actuator design proposed here embodies a low-power implementation that is well suited to integration with newly constructed blades and potentially for retrofit onto existing systems. The projected cost of this class of devices is well within the parameters identified in the literature as being consistent with real-world installations. The work to be proposed would perform initial development of this load control system, which would leverage both lessons learned from prior implementation of on-blade control surfaces for wind turbines and rotorcraft as well as major elements of condition monitoring methods developed for air vehicle applications. The projected technical objectives for the Phase I effort would be to: 1) establish tradeoffs between actuator response speed/cycles and turbine blade lifespan/fatigue loads; 2) establish actuator and device scaling; 3) estimate device lifespan based on actuation response and projections of operational loads and resilience to damage; and 4) develop a provisional manufacturing/blade integration plan. The team would include actuation device design, scaling, and cycle life analysis expertise from Continuum Dynamics, Inc., along with overall project technical direction; critical support on identifying designs that could maximize blade life extension would be provided by Sandia National Laboratories; and guidance both from Sandia and TPI Composites regarding requirements and methods for integration the projected actuators into practical blade designs. The Phase I proof of concept effort would lay the foundation for both demonstration integration efforts on turbine blades as well as larger scale testing in Phase II. The principal immediate application of this work is to provide additional control mechanisms to improve the reliability and life of wind turbine blades and systems. The actuator and adaptive control system technology to be developed as part of this effort could be used for new turbine designs and also be applied to retrofit existing wind energy systems for improved performance and structural life. The principal immediate application of this work is to provide additional control mechanisms to improve the efficiency and reliability of wind turbine rotors and wind turbine systems. The actuator and adaptive control system technology to be developed as part of this effort could be used for new turbine designs and also be applied to retrofit existing wind energy systems for improved performance and structural life. The net effect of their use would support reducing the operating costs of wind turbines, thereby improving their power conversion capability and enhancing their power quality.
Agency: Department of Energy | Branch: | Program: STTR | Phase: Phase I | Award Amount: 149.92K | Year: 2015
Wind power plays an increasingly important role in satisfying the power needs of the U.S., and serves to reduce dependence on fossil fuels. With increased penetration, significant maintenance costs and reductions in power generation have underscored the need to predict the unsteady loading related to turbine configuration, layout and off-design wind conditions as well as importance of accounting for inter-turbine interactions in wind farms. Contemporary turbine design tools fail to account for the unsteady fluid structure interactions that drive costly fatigue loads, and thus, the research community has started utilizing High Performance Computing (HPC) solvers to investigate these phenomena. Unfortunately, such tools often require dedicated technical experts to generate reliable predictions and are too complicated and expensive for general industrial use. This problem is exacerbated for wind turbines given the unsteady coupling between blade motion, flexibility, wake aerodynamics and the interaction with other turbines and the turbulent atmosphere. In a recently completed DOE STTR, Continuum Dynamics, Inc. (CDI) and Georgia Institute of Technology (GIT) developed an advanced method for predicting wind turbine fatigue and wind farm aeromechanics. While this effort successfully demonstrated improved analysis capabilities, the HPC-based methods still require expert users to exploit their capabilities. The proposed effort builds upon this prior work and the experience of CDI and GIT in developing numerical methods, along with collaborators in the wind energy industry (NREL), to extend, harden and ultimately transition these numerical methods to industry. Phase I would commence addressing critical code hardening issues such asreliable MPI error handling, automated input generation and checking, and throughput optimization. One of themost significant hurdles to transitioning solvers to industry is that while many HPC-level solvers are very capable, they require complete adoption, whereby legacy software is relegated to the scrap-heap. Given significant investment in legacy software, this barrier is often insurmountable, and can be seen throughout the industry where simplified models are used for routine engineering. CDI has adopted a successful modular software strategy to address this barrier, where advanced solvers components are packaged as libraries, thus enabling industry to adopt the improved numerical methods without the loss of institutional knowledge. Through standardized interfaces, this, in effect, facilitates the development of traceable, hierarchical HPC analysis tools that no longer need expert users. In this vein, Phase I would culminate with the proof-of-concept interfacing between components of the wind turbine aeromechanics methods with NRELs industry standard wind turbine computer-aided engineering code FAST.Commercial Applications and Other Benefits: A successful STTR effort would produce a robust, validated multidisciplinary computational tool for integrated wind turbine design and analysis, along with individual solver libraries for more general application. This tool directly addresses the limitations of current HPC CFD techniques for predicting FSI problems such as unsteady turbine blade loading and situational interactions. Based upon a modest market entry, combined sales, and associated service work, could generate ~$3M in sales over several years, with major cost savings attributed to improved prediction of FSI to customers and lower maintenance costs for end users. Moreover, as is evidenced by the included letter of support, additional commercialization is anticipated through application to other vorticity dominated flow filed such as rotorcraft, automotive and bluff-bodies.