Publications

Plants as Factories for Technical Materials

Until the latter part of the 19th century, humans were largely dependent upon contemporaneous biological sources for the production of all organic materials. Plants and animals provided the only sources of fibers, coatings, lubricants, solvents, dyes, waxes, fillers, and insulation, fragrances,

Improving Outcome of Psychosocial Treatments by Enhancing Memory and Learning

Mental disorders are prevalent and can lead to significant impairment. Some progress has been made toward establishing treatments; however, effect sizes are small to moderate, gains may not persist, and many patients derive no benefit. Our goal is to highlight the potential for empirically supported psychosocial treatments to be improved by incorporating insights from cognitive psychology and research on education. Our central question is: If it were possible to improve memory for the content of sessions of psychosocial treatments, would outcome substantially improve? We leverage insights from scientific knowledge on learning and memory to derive strategies for transdiagnostic and transtreatment cognitive support interventions. These strategies can be applied within and between sessions and to interventions delivered via computer, the Internet, and text message. Additional novel pathways to improving memory include improving sleep, engaging in exercise, and using imagery. Given that memory processes change across the lifespan, services to children and older adults may benefit from different types and amounts of cognitive support.

Learning Shape Abstractions by Assembling Volumetric Primitives

We present a learning framework for abstracting complex shapes by learning to assemble objects using 3D volumetric primitives. In addition to generating simple and geometrically interpretable explanations of 3D objects, our framework also allows us to automatically discover and exploit consistent structure in the data. We demonstrate that using our method allows predicting shape representations which can be leveraged for obtaining a consistent parsing across the instances of a shape collection and constructing an interpretable shape similarity measure. We also examine applications for image-based prediction as well as shape manipulation.

Nighttime ACTH, cortisol, prolactin, and growth hormone secretion in prepubertal depression

Supernovae 2008H and 2008I

CCDC 265836: Experimental Crystal Structure Determination

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

An Integrated Computational and Experimental Approach Toward the Design of Materials for Fuel Cell Systems

Abstract : The MURI set out with a series of objectives to construct a theory toolkit coupled to advanced experimentation for validation and support. We have achieved all of our initial objectives in this regard and have expanded the scope of the MURI to use theory and experimentation to drive the prediction and preparation of new and highly active catalysts for key processes in fuel cells. Succinctly stated, our theory and experimental goals were as follows: Theory Objectives: *Accurate Quantum Mechanical Methods for Kinetics and thermodynamics *In silico Synthesis of Particle Structure *Quantum Mechanical Electrocatalysis *Ab initio Descriptions of Electron/Proton Transfer *Predictive Catalysis: Multiscale Catalysis Model *Data Mining Approaches to Predict New Materials. Experimental Objectives: *Theory Support *Studies of Key Electrocatalytic Processes *New Catalysts *New Experimental Characterization of Structure All of these objectives were achieved in the course of this project. We have reported a long series of innovations and, indeed, have extended this original list. Several of the investigators in the team have been cited as among the most productive ARO contractors.

Synthesis, Characterization, and Reactivity of Monomeric, Arylpalladium Halide Complexes with a Hindered Phosphine as the Only Dative Ligand

We report the isolation and structural characterization of several monomeric arylpalladium(II) halide complexes containing tri-tert-butyl phosphine, 1-adamantyl-di-tert-butylphosphine, or 2-adamantyl-di-tert-butylphosphine. X-ray diffraction, IR spectroscopy, and theoretical studies indicated that the complexes may be stabilized by agostic interactions. For example, the distance from the closest hydrogen atom to the palladium metal center in the X-ray structure of the 1-adamantyl-phenylpalladium bromide complex 1 was 2.26(3) A. The calculated Pd-H distance of 2.28 A and harmonic vibrational frequencies were in agreement with the measured distance, but Wiberg bond indices indicated only weak M-H-C interactions. Addition of 2-adamantyl-di-tert-butyl phosphine to 1 led to ligand exchange and formation of 2-adamantyl-di-tert-butyl phosphine complex 2. Addition of P(t-Bu)(3) generated free aryl bromide and Pd[P(t-Bu)(3)](2). Reactivity of complex 1 with nucleophiles provided evidence of the intermediacy of these complexes in palladium-catalyzed cross-coupling reactions. Complex 1 reacted with amine and base to form the corresponding arylamine, with tert-butoxide to form the corresponding ether, with boronic acid and fluoride to form the corresponding biaryl, and with styrene to form stilbene. This complex also catalyzed the reaction of bromobenzene with diphenylamine in the presence of base to produce 94% of the amination product in 45 min at room temperature. This rate is comparable to the reaction rate of in situ generated catalysts.

National Science Foundation-Sponsored Workshop Report: “The 2010 Project”Functional Genomics and the Virtual Plant. A Blueprint for Understanding How Plants Are Built and How to Improve Them

Although future developments in a rapidly emerging field can be difficult to predict, some projections and evaluations are helpful in planning for the development of community resources and other initiatives that may facilitate progress. To make these projections and evaluations, a group of scientists met at The Salk Institute for Biological Studies, La Jolla, CA, on January 13 and 14, 2000. The workshop, co-chaired by Joanne Chory and Joseph Ecker, included the following group of scientists: Steven Briggs, Michel Caboche, Gloria Coruzzi, Doug Cook, Jeff Dangl, Sarah Grant, Mary Lou Guerinot, Steven Henikoff, Rob Martienssen, Kiyotaka Okada, Natasha Raikhel, Chris Somerville, and Detlef Weigel.

Understanding Photovoltage Enhancement in Metal–Insulator Semiconductor Photoelectrodes with Metal Nanoparticles

A metal-insulator-semiconductor (MIS) structure holds great potential to promote photoelectrochemical (PEC) reactions, such as water splitting and CO₂ reduction, for the storage of solar energy in chemical bonds. The semiconductor absorbs photons, creating electron-hole pairs; the insulator facilitates charge separation; and the metal collects the desired charge and facilitates its use in the electrochemical reaction. Despite these attractive features, MIS photoelectrodes are significantly limited by their photovoltage, a combination of the voltage generated from photon absorption minus the potential drop across the insulator. Herein, we use multiscale continuum modeling of the carrier, electrolyte, and interfacial transport to identify strategies for mitigating the deleterious potential drop across the insulator and enabling high MIS photovoltages. To this end, we model Ni/SiO₂/n-Si photoanodes that employ a planar Ni film or Ni nanoparticles (np-MIS) and validate both models using experimental polarization curves and photovoltage measurements from the literature. The simulations reveal that the insulator potential drop is lower and hence achieves higher photovoltages for np-MIS structures than MIS structures because the electrolyte screens charge trapped at defect states between the semiconductor and the insulator. This electrolyte charge screening phenomenon can be further leveraged by using low loadings or small nanoparticles, which not only minimize the interfacial potential drop but also improve the photocurrent by enabling more light absorption. These insights contribute to the optimization of the np-MIS structures for sustainable energy conversion.

Functional analysis of the COBRA-like family

The COBRA protein is found only in higher plants and algae, and has been implicated in cellulose synthesis, but its specific function remains unknown. To shed light on COBRA function we tested the ability of putative Arabidopsis COBRA orthologs to complement mutations in the COBRA gene. We expanded the previously published phylogenetic analysis and found that COBRA genes can be grouped into five clades. Representative COBRA genes from the different clades were expressed in a cobra mutant background. Surprisingly, none of the COBRA-LIKE genes was able to complement cobra, including the closest homolog which we found to bind cellulose with the same avidity as COBRA. We hypothesize that the lack of ability of the COBRA-LIKE genes to complement the cobra mutant is due to an unidentified binding interaction that is sensitive to the structure of the COBRA-LIKE proteins. However, membrane-based yeast two hybrid assays failed to identify positive interactors for COBRA.

The effects of parasitic reactances on nonlinear networks

This paper considers several of the problems caused by the presence of small parasitic capacitances and inductances in nonlinear network models. It first gives the condition for which the behavior of a network model can be approximated by the behavior of a simplified model recently with the parasitics removed. The condition is that the resistive subnetwork viewed from the terminals of the parasitics be strictly locally passive for a certain set of currents and voltages. This condition is independent of the relative magnitudes of the parasitics. The paper then considers networks whose equations cannot be put into normal form without the addition of a parasitic. In the case where two different choices of parasitics enable the network equations to be put into normal form, it gives conditions on the resistive subnetwork which ensure that the behavior of the two resulting networks is the same. It then exhibits a class of networks such that the networks resulting from the addition of any choice of parasitic which enables the network equations to be put into normal form have the same behavior. Finally, the paper shows how the behavior of this class of networks can be determined without the addition of parasitics. It formulates an inertia postulate and an explicit jump postulate to enable the multivalued normal form equations to be solved unambiguously.

Macroporous polymeric stationary-phase rod as continuous separation medium for reversed-phase chromatography

A macroporous poly(styrene-co-divinylbenzene) rod has been prepared by a free-radical polymerization of a mixture containing monomers, initiator, and porogenic solvent in the confines of a chromatographic column and used for the first time in the very fast reversed-phase HPLC of proteins. Characterization of the pore structure of the continuous rod by mercury intrusion porosimetry revealed a large volume of pores with a diameter of about 1 micron to pores below 100 nm. Size exclusion chromatography and scanning electron microscopy confirmed the unusual pore size distribution. The presence of large pores make the rod easily permeable to eluents, and therefore, the back pressure of the rod column is modest even at high flow rates. The efficiency of the polymerized column is almost independent of the flow rate. The slope of the line showing capacity factor vs composition of the mobile phase was determined for several proteins, and a gradient for the separation of their mixtures was developed. Excellent separation was achieved even at a high flow rate of 25 mL/min as documented by the resolution data. Tripling the length of the column did not improve the column resolution in protein separation.

Recombinant protein synthesis and isolation of human interferon alpha-2 in cyanobacteria

Femtosecond Transient Absorption Studies of Energy Transfer within Chromophore-Labeled Dendrimers

Dendrimers possessing coumarin-2 dyes at the periphery, and either a coumarin-343 or a heptathiophene dye at the core, have been studied by femtosecond transient absorption spectroscopy in order to elucidate energy-transfer rate constants. These measurements indicated that energy transfer occurs with average correlation times of less than 6 ps in the first three generations, and slows to a correlation time of approximately 18 ps in the fourth. The transient spectral features arising from excitation of the peripheral donor chromophores at 330 nm are described. Additionally, these measurements provide a quantitative comparison between observed and theoretical energy-transfer rate constants (kET), indicating a close correlation of the experimental results with Förster theory.

AFM study of surface morphology of segmented polyurethane block copolymers and their blends with phenoxy

AFM was used to investigate the surface morphology and surface modification effects of newly developed segmented polyurethanes and their mixture with phenoxy homopolymer. The polyurethanes were methylene diisocyanate (MDI) and polytetramethyleneoxide (PTMO) based polymer with low surface tension end groups of polydimethysiloxane (PDMS). Two types of surface structures were observed from polyurethanes, a number of holes with a wide range of sizes, presumably due to the large soft segment molecular weight, and fine granular structures on the terraces. The PDMS end groups formed these fine granular structure and made the surface roughness smaller compared to polyurethanes without PDMS. The surface modification effect of polyurethanes was also investigated. The polymer mixtures of polyurethane and phenoxy indicated phase separation of the blends. The surface was composed of two phases, honeycomb polyurethane rich phase and dispersed phenoxy rich phase. The polyurethane rich phase tended to segregate on the surface. The honeycomb phase increased in thickness and area fraction when the polyurethane concentration was increased.

Low gap amorphous GaN1−xAsx alloys grown on glass substrate

Amorphous GaN1−xAsx layers with As content in the range of x=0.1 to 0.6 were grown by molecular beam epitaxy on Pyrex glass substrate. These alloys exhibit a wide range of band gap values from 2.2 to 1.3 eV. We found that the density of the amorphous films is ∼0.8–0.85 of their corresponding crystalline value. These amorphous films have smooth morphology, homogeneous composition, and sharp well defined optical absorption edges. The measured band gap values for the crystalline and amorphous GaN1−xAsx alloys are in excellent agreement with the predictions of the band anticrossing model. The high absorption coefficient of ∼105 cm−1 for the amorphous GaN1−xAsx films suggests that relatively thin films (on the order of 1 μm) are necessary for photovoltaic application.

Tunable energy landscape of screw dislocation cores by compositional fluctuations in bcc high-entropy alloys from first-principles calculations

The energy landscape of screw dislocation cores plays a central role in dislocation-mediated deformation mechanisms in body-centered cubic (bcc) metals. In bcc high-entropy alloys (HEAs), this energy landscape is modulated by local compositional fluctuations, which has important implications for deformation processes in these materials. Through first-principles calculations, this study investigates high-symmetry screw dislocation core structures in NbTaMoW and NbTaTiHf bcc HEAs. The results show that alloying group IV transition metals lead to large local lattice distortions at dislocation cores, which is demonstrated to be an important factor governing fluctuations in core configurations along a dislocation line. Importantly, group IV elements near the core induce features in the energy landscape that are exclusive for HEAs, specifically lowering the energy of core configurations that are unstable in elemental bcc metals. A combined influence of these chemical effects with crystallographic details enables the activation of <a:math xmlns:a="http://www.w3.org/1998/Math/MathML"><a:mrow><a:mo>{</a:mo><a:mn>112</a:mn><a:mo>}</a:mo></a:mrow></a:math> glide planes, a feature that has been linked to ductility improvements in bcc HEAs. These findings provide new insights into the atomic-scale mechanisms underlying dislocation mobility in bcc HEAs, offering a pathway for designing materials with tailored mechanical properties.