There has been a concerted effort since 2007 to establish a dashboard of metrics for the Science, Technology, and Engineering (ST&E) work at Sandia National Laboratories. These metrics are to provide a self assessment mechanism for the ST&E Strategic Management Unit (SMU) to complement external expert review and advice and various internal self assessment processes. The data and analysis will help ST&E Managers plan, implement, and track strategies and work in order to support the critical success factors of nurturing core science and enabling laboratory missions. The purpose of this SAND report is to provide a guide for those who want to understand the ST&E SMU metrics process. This report provides an overview of why the ST&E SMU wants a dashboard of metrics, some background on metrics for ST&E programs from existing literature and past Sandia metrics efforts, a summary of work completed to date, specifics on the portfolio of metrics that have been chosen and the implementation process that has been followed, and plans for the coming year to improve the ST&E SMU metrics process.
This highly interdisciplinary team has developed dual-color, total internal reflection microscopy (TIRF-M) methods that enable us to optically detect and track in real time protein migration and clustering at membrane interfaces. By coupling TIRF-M with advanced analysis techniques (image correlation spectroscopy, single particle tracking) we have captured subtle changes in membrane organization that characterize immune responses. We have used this approach to elucidate the initial stages of cell activation in the IgE signaling network of mast cells and the Toll-like receptor (TLR-4) response in macrophages stimulated by bacteria. To help interpret these measurements, we have undertaken a computational modeling effort to connect the protein motion and lipid interactions. This work provides a deeper understanding of the initial stages of cellular response to external agents, including dynamics of interaction of key components in the signaling network at the 'immunological synapse,' the contact region of the cell and its adversary.
Fluorescence correlation spectroscopy (FCS) is used to examine mobility of labeled probes at specific sites in supported bilayers consisting of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) lipid domains in 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). Those sites are mapped beforehand with simultaneous atomic force microscopy and submicron confocal fluorescence imaging, allowing characterization of probe partitioning between gel DPPC and disordered liquid DOPC domains with corresponding topography of domain structure. We thus examine the relative partitioning and mobility in gel and disordered liquid phases for headgroup- and tailgroup-labeled GM1 ganglioside probes and for headgroup- and tailgroup-labeled phospholipid probes. For the GM1 probes, large differences in mobility between fluid and gel domains are observed; whereas unexpected mobility is observed in submicron gel domains for the phospholipid probes. We attribute the latter to domain heterogeneities that could be induced by the probe. Furthermore, fits to the FCS data for the phospholipid probes in the DOPC fluid phase require two components (fast and slow). Although proximity to the glass substrate may be a factor, local distortion of the probe by the fluorophore could also be important. Overall, we observe nonideal aspects of phospholipid probe mobility and partitioning that may not be restricted to supported bilayers.
We present our research results on membrane pores. The study was divided into two primary sections. The first involved the formation of protein pores in free-standing lipid bilayer membranes. The second involved the fabrication via surface micromachining techniques and subsequent testing of solid-state nanopores using the same characterization apparatus and procedures as that used for the protein pores. We were successful in our ability to form leak-free lipid bilayers, to detect the formation of single protein pores, and to monitor the translocation dynamics of individual homogeneous 100 base strands of DNA. Differences in translocation dynamics were observed when the base was switched from adenine to cytosine. The solid state pores (2-5 nm estimated) were fabricated in thin silicon nitride membranes. Testing of the solid sate pores indicated comparable currents for the same size protein pore with excellent noise and sensitivity. However, there were no conditions under which DNA translocation was observed. After considerable effort, we reached the unproven conclusion that multiple (<1 nm) pores were formed in the nitride membrane, thus explaining both the current sensitivity and the lack of DNA translocation blockages.
This project set out to scientifically-tailor ''smart'' interfacial films and 3-D composite nanostructures to exhibit photochromic responses to specific, highly-localized chemical and/or mechanical stimuli, and to integrate them into optical microsystems. The project involved the design of functionalized chromophoric self-assembled materials that possessed intense and environmentally-sensitive optical properties (absorbance, fluorescence) enabling their use as detectors of specific stimuli and transducers when interfaced with optical probes. The conjugated polymer polydiacetylene (PDA) proved to be the most promising material in many respects, although it had some drawbacks concerning reversibility. Throughout his work we used multi-task scanning probes (AFM, NSOM), offering simultaneous optical and interfacial force capabilities, to actuate and characterize the PDA with localized and specific interactions for detailed characterization of physical mechanisms and parameters. In addition to forming high quality mono-, bi-, and tri-layers of PDA via Langmuir-Blodgett deposition, we were successful in using the diacetylene monomer precursor as a surfactant that directed the self-assembly of an ordered, mesostructured inorganic host matrix. Remarkably, the diacetylene was polymerized in the matrix, thus providing a PDA-silica composite. The inorganic matrix serves as a perm-selective barrier to chemical and biological agents and provides structural support for improved material durability in microsystems. Our original goal was to use the composite films as a direct interface with microscale devices as optical elements (e.g., intracavity mirrors, diffraction gratings), taking advantage of the very high sensitivity of device performance to real-time dielectric changes in the films. However, our optical physics colleagues (M. Crawford and S. Kemme) were unsuccessful in these efforts, mainly due to the poor optical quality of the composite films.
The intention of this project was to collaborate with Harvard University in the general area of nanoscale structures, biomolecular materials and their application in support of Sandia's MEMS technology. The expertise at Harvard was crucial in fostering these fundamentally interdisciplinary developments. Areas that were of interest included: (1) nanofabrication that exploits traditional methods (from Si technology) and developing new methods; (2) self-assembly of organic and inorganic systems; (3) assembly and dynamics of membranes and microfluidics; (4) study of the hierarchy of scales in assembly; (5) innovative imaging methods; and (6) hard (engineering)/soft (biological) interfaces. Specifically, we decided to work with Harvard to design and construct an experimental test station to measure molecular transport through single nanopores. The pore may be of natural origin, such as a self-assembled bacterial protein in a lipid bilayer, or an artificial structure in silicon or silicon nitride.
The authors use scanning probe microscopy to actuate and characterize the nanoscale mechanochromism of polydiacetylene monolayer on atomically-flat silicon oxide substrates. They find explicit evidence that the irreversible blue-to-red transformation is caused by shear forces exerted normal to the polydiacetylene polymer backbone. The anisotropic probe-induced transformation is characterized by a significant change in the tilt orientation of the side chains with respect to the surface normal. They also describe a new technique, based on shear force microscopy, that allows them to image friction anisotropy of polydiacetylene monolayer independent of scan direction. Finally, they discuss preliminary molecular mechanics modeling and electronic structure calculations that allow them to understand the correlation of mechanochromism with bond-angle changes in the conjugated polymer backbone.
We have investigated the thermochromic transition of an ultrathin poly(diacetylene) film. The Langmuir film is composed of three layers of polymerized 10,12-pentacosadiynoic acid organized into crystalline domains on a silicon substrate. Spectroscopic ellipsometry and fluorescence intensity measurements are obtained with in situ temperature control. Poly-PCDA films exhibit a reversible thermal transition between the initial blue form and an intermediate 'purple' form that exists only at elevated temperature (between 303 and 333 K), followed by an irreversible transition to the red form after annealing above 320 K. We propose that the purple form is thermally distorted blue poly-PCDA and may represent a transitional configuration in the irreversible conversion to red. This hypothesis is supported by the appearance of unique features in the absorption spectra for each form as derived from the ellipsometry measurements. Significant fluorescence emission occurs only with the red form and is reduced at elevated temperatures while the absorption remains unchanged. Reduced emission is likely related to thermal fluctuations of the hydrocarbon side chains. Time-resolved fluorescence measurements of the irreversible transition have been performed. Using a first-order kinetic analysis of these measurements, we deduce an energy barrier of 17.6 ± 1.1 kcal mol-1 between the blue and red forms.
The ability to create organized ultrathin films using organic molecules provides systems whose chemical, mechanical, and optical properties can be controlled for specific applications. In particular, polymerization of oriented mono- and multi-layer films containing the diacetylene group has produced a variety of robust, highly oriented, and environmentally responsive films with unique chromatic properties. These two-dimensional poly(diacetylene) (PDA) films, where the conjugation runs parallel to the film surface, have previously been prepared in a variety of forms. Of particular interest is the optical absorption of PDA due to its {pi}-conjugated backbone. A wide variety of PDA materials, including bulk crystals, thin films, and solutions, exhibit a chromatic transition involving a significant shift in absorption from low to high energy bands of the visible spectrum, thus the PDA appears to transform from a blue to a red color. In addition, the red form is highly fluorescent, while the blue form is not. This transition can be brought about by heat binding of specific biological targets and applied stress (mechanochromism), among others. In this paper, the authors discuss the Langmuir deposition of ultrathin PDA films and the subsequent measurement of their structural, optical, and mechanical properties at the nanometer scale. By altering the head group functionality, the authors can choose between mono- and tri-layer PDA film structures. Measurements with the atomic force microscope (AFM) reveal strongly anisotropic friction properties that are correlated with the orientation of the conjugated polymer backbone orientation. Furthermore, the authors can use the AFM tip or a near field scanning optical microscope (NSOM) tip to locally convert the PDA from the blue form to the red form via applied stress. This represents the first time that mechanochromism has been observed at the nanometer scale. Dramatic structural changes are associated with this mechanochromic transition.
Atomically flat monolayer and trilayer films of polydiacetylenes have been prepared on mica and silicon using a horizontal deposition technique from a pure water subphase. Langmuir films of 10,12-pentacosadiynoic acid (I) and N-(2-ethanol)-10,12-pentacosadiynamide (II) were compressed to 20 mN/m and subsequently polymerized by UV irradiation at the air-water interface. Blue and red forms of the films were prepared by varying exposure times and incident power. Polymerization to the blue-phase films produced slight contractions in the film of 2 and 5% for the films of II and I, respectively. Longer UV exposures yielded red-phase films with dramatic film contraction of 15 and 32% for II and I, respectively. The horizontal deposition technique provided transfer ratios of unity with minimal film stress or structure modification. Atomic force microscopy images revealed nearly complete coverage of the substrate with atomically flat films. Crystalline domains of up to 100 microns of highly oriented polydiacetylene molecules were observed. The results reported herein provided insight into the roles of molecular packing and chain orientations in converting the monomeric film to the polymerized blue- and red-phases.