Here, self-assembled monolayers (SAMS) have been investigated for their ability to confine the absorption of the motor protein kinesin and direct the movement of microtubule shuttles (MTs) within channels of a lithographically patterned microfluidic device. Channels were made from gold films deposited on a silicon wafer to provide chemically distinct surfaces for the selective formation of a range of alkane thiol monolayers on channel walls. Devices were then exposed to solutions containing casein and kinesin to develop protein monolayers capable of propelling microtubules in the presence of adenosine triphosphate (ATP) fuel. Fluorescence microscopy images were used to observe the attachment of MTs to chemically distinct regions and to evaluate the ability of the various monolayer coatings to confine the movement of MTs within the channel system. Ellipsometry was used to characterize the protein adsorption characteristics of SAMS terminated with different functional groups to help establish confinement mechanisms. Finally, both anti-fouling and cationic monolayers were found to be effective in confining MT movement within the channels by controlling the adsorption or orientation of the casein buffer layers that mediate motor protein attachment and functionality.
Since 1998, the Department of Energy/NNSA National Laboratories have invested millions in strategies for assessing the credibility of computational science and engineering (CSE) models used in high consequence decision making. The answer? There is no answer. There's a process--and a lot of politics. The importance of model evaluation (verification, validation, uncertainty quantification, and assessment) increases in direct proportion to the significance of the model as input to a decision. Other fields, including computational social science, can learn from the experience of the national laboratories. Some implications for evaluating 'low cognition agents'. Epistemology considers the question, How do we know what we [think we] know? What makes Western science special in producing reliable, predictive knowledge about the world? V&V takes epistemology out of the realm of thought and puts it into practice. What is the role of modeling and simulation in the production of reliable, credible scientific knowledge about the world? What steps, investments, practices do I pursue to convince myself that the model I have developed is producing credible knowledge?
The Sandia National Laboratories, California (SNL/CA) Environmental Management System (EMS) Program Manual documents the elements of the site EMS Program. The SNL/CA EMS Program conforms to the International Standard on Environmental Management Systems, ISO 14001:2004. Elements of the ISO standard overlap with those of Department of Energy (DOE) Order 450.1, thus SNL/CA's EMS program also meets the DOE requirements.
Aria is a Galerkin finite element based program for solving coupled-physics problems described by systems of PDEs and is capable of solving nonlinear, implicit, transient and direct-to-steady state problems in two and three dimensions on parallel architectures. The suite of physics currently supported by Aria includes the incompressible Navier-Stokes equations, energy transport equation, species transport equations, nonlinear elastic solid mechanics, and electrostatics as well as generalized scalar, vector and tensor transport equations. Additionally, Aria includes support for arbitrary Lagrangian-Eulerian (ALE) and level set based free and moving boundary tracking. Coupled physics problems are solved in several ways including fully-coupled Newton's method with analytic or numerical sensitivities, fully-coupled Newton-Krylov methods, fully-coupled Picard's method, and a loosely-coupled nonlinear iteration about subsets of the system that are solved using combinations of the aforementioned methods. Error estimation, uniform and dynamic h-adaptivity and dynamic load balancing are some of Aria's more advanced capabilities. Aria is based on the Sierra Framework.
In recent years, considerable effort has been placed on developing efficient and robust solution algorithms for the incompressible Navier-Stokes equations based on preconditioned Krylov methods. These include physics-based methods, such as SIMPLE, and purely algebraic preconditioners based on the approximation of the Schur complement. All these techniques can be represented as approximate block factorization (ABF) type preconditioners. The goal is to decompose the application of the preconditioner into simplified sub-systems in which scalable multi-level type solvers can be applied. In this paper we develop a taxonomy of these ideas based on an adaptation of a generalized approximate factorization of the Navier-Stokes system first presented in [25]. This taxonomy illuminates the similarities and differences among these preconditioners and the central role played by efficient approximation of certain Schur complement operators. We then present a parallel computational study that examines the performance of these methods and compares them to an additive Schwarz domain decomposition (DD) algorithm. Results are presented for two and three-dimensional steady state problems for enclosed domains and inflow/outflow systems on both structured and unstructured meshes. The numerical experiments are performed using MPSalsa, a stabilized finite element code.
In this paper, a system model is developed to investigate independent and coupled effects of resolution, noise and data processing algorithms on the accuracy of the scalar gradient and dissipation measurements in turbulent flows. Finite resolution effects are simulated by spectral filtering, noise is modelled as an additive source in the model spectrum and differencing stencils are analysed as digital filters. In the current study, the effective resolution is proposed to be a proper criterion for quantifying the resolution requirement for scalar gradient and dissipation measurement. Both effective resolution and noise-induced apparent dissipation are mainly determined by the system transfer function. The finite resolution results, based upon a model scalar energy spectrum, are shown to agree with non-reacting experimental data. The coupled resolution-noise results show three regions in the mean scalar dissipation rate measurement: noise-dominated region, noise-resolution correlated region and resolution-dominated region. Different noise levels lead to different resolution error curves for the measured mean scalar dissipation rate. Experimental procedures and guidelines to improve the scalar gradient and dissipation experiments are proposed, based on these model study results. Finally, the proposed system approach can also be applied to other derived quantities involving complex transfer functions.
Robots for high-force interaction with humans face particular challenges to achieve performance and coupled stability. Because available actuators are unable to provide sufficiently high force density and low impedance, controllers for such machines often attempt to mask the robots physical dynamics, though this threatens stability. Controlling for passivity, the state-of-the-art means of ensuring coupled stability, inherently limits performance to levels that are often unacceptable. A controller that imposes passivity is compared to a controller designed by a new method that uses limited knowledge of human dynamics to improve performance. Both controllers were implemented on a testbed, and coupled stability and performance were tested. Results show that the new controller can improve both stability and performance. The different structures of the controllers yield key differences in physical behavior, and guidelines are provided to assist in choosing the appropriate approach for specific applications.
Modeling contagious diseases has taken on greater importance over the past several years as diseases such as SARS and avian influenza have raised concern about worldwide pandemics. Most models developed to consider projected outbreaks have been specific to a single disease. This paper describes a generic System Dynamics contagious disease model and its application to human-to-human transmission of a mutant version of avian influenza. The model offers the option of calculating rates of new infections over time based either on a fixed ''reproductive number'' that is traditional in contagious disease models or on contact rates for different sub-populations and likelihood of transmission per contact. The paper reports on results with various types of interventions. These results suggest the potential importance of contact tracing, limited quarantine, and targeted vaccination strategies as methods for controlling outbreaks, especially when vaccine supplies may initially be limited and the efficacy of anti-viral drugs uncertain.
The Waste Management Symposium 2007 is the most recent in a long series that has been held at Tucson, Arizona. The meeting has become extremely popular as a venue for technical exchange, marketing, and networking involving upward of 1800 persons involved with various aspects of radioactive waste management. However, in a break with tradition, the symposium organizers reported that next year’s Waste Management Symposium would be held at the Phoenix, AZ convention center. Additionally, most of the WM07 sessions dealt with the technical and institutional issues relating to the resolution of waste disposal and processing challenges, including a number of sessions dealing with related transport activities.