Mechanisms of the Photomechanical Response in Thin-Film Dye-Doped Glassy Polymers.

This work aims to determine the mechanism of the photomechanical response of poly(Methyl methacrylate) polymer doped with the photo-isomerizable dye Disperse Red 1 using the non-isomerizable dye Disperse Orange 11 as a control to isolate photoisomerization. Samples are free-standing thin films with thickness that is small compared with the optical skin depth to assure uniform illumination and photomechanical response throughout their volume, which differentiates these studies from most others. Polarization-dependent measurements of the photomechanical stress response are used to deconvolute the contributions of angular hole burning, molecular reorientation and photothermal heating.

Imaging studies of photodegradation and self-healing in anthraquinone derivative dye-doped PMMA.

We study photodegradation and self-healing of nine different anthraquinone-derivatives doped into PMMA using transmission imaging microscopy in search of structure-property relationships of the underlying mechanisms. We find that seven of the nine anthraquinone derivatives display partially reversible photodegradation, with 1,8-dihydroxyanthraquinone (Dantron/Chrysazin) having the best photostability and recovery characteristics of all dyes tested in this study. Based on these measurements we predict that a sample of 1,8-dihydroxyanthraquinone doped into PMMA with a concentration of 9 g l-1 will have a record setting irreversible inverse quantum efficiency of Bε = 4.

Using a proxy state to improve the accuracy of truncated hyperpolarizability calculations.

We present a simple algorithm for defining a single proxy state that accounts for state truncation in the sum-over-states calculations of the dispersion of the molecular hyperpolarizabilities. The transition strengths between the proxy state and the truncated set of states are determined using the Thomas-Reiche-Kuhn sum rules further constrained by the zero-frequency linear polarizability. This proxy state method can augment experimentally determined parameters or finite-state theories to allow for a more accurate prediction of the nonlinear optical properties of molecular systems.

Exact Fundamental Limits of the First and Second Hyperpolarizabilities.

Nonlinear optical interactions of light with materials originate in the microscopic response of the molecular constituents to excitation by an optical field, and are expressed by the first (β) and second (γ) hyperpolarizabilities. Upper bounds to these quantities were derived seventeen years ago using approximate, truncated state models that violated completeness and unitarity, and far exceed those achieved by potential optimization of analytical systems. This Letter determines the fundamental limits of the first and second hyperpolarizability tensors using Monte Carlo sampling of energy spectra and transition moments constrained by the diagonal Thomas-Reiche-Kuhn (TRK) sum rules and filtered by the off-diagonal TRK sum rules.

Imaging studies of temperature dependent photodegradation and self-healing in disperse orange 11 dye-doped polymers.

Using confocal transmission imaging microscopy, we measure the temperature dependence of photodegradation and self-healing in disperse orange 11 (DO11) dye-doped (poly)methyl-methacrylate (PMMA) and polystyrene (PS). In both dye-doped polymers, an increase in sample temperature results in a greater photodegradation rate and degree of degradation, while also resulting in a slower recovery rate and larger recovery fraction. These results confirm the temperature dependence predictions of the modified correlated chromophore domain model (mCCDM) [B.

Time-Domain Simulation of Three Dimensional Quantum Wires.

A method is presented to calculate the eigenenergies and eigenfunctions of quantum wires. This is a true three-dimensional method based on a direct implementation of the time-dependent Schrödinger equation. It makes no approximations to the Schrödinger equation other than the finite-difference approximation of the space and time derivatives.

Spectroscopic studies of the mechanism of reversible photodegradation of 1-substituted aminoanthraquinone-doped polymers.

The mechanism of reversible photodegradation of 1-substituted aminoanthraquinones doped into poly(methyl methacrylate) and polystyrene is investigated. Time-dependent density functional theory is employed to predict the transition energies and corresponding oscillator strengths of the proposed reversibly and irreversibly damaged dye species. Ultraviolet-visible and Fourier transform infrared (FTIR) spectroscopy are used to characterize which species are present.

Chip-based silica microspheres for cavity optomechanics.

We have experimentally realized on-chip silica microspheres that feature excellent thermal coupling to the silicon wafer. The chip-based microspheres significantly reduce laser-induced heating and correspondingly exhibit much lower threshold optical power for heating-induced optical bistability. We also show that the chip-based microspheres have optical and especially optomechanical properties that are similar to those of traditional fiber-stem-attached silica microspheres, making the chip-based microspheres suitable for optomechanical studies in a vacuum environment.

Phase disruption as a new design paradigm for optimizing the nonlinear-optical response.

The intrinsic optical nonlinearities of linear structures, including conjugated chain polymers and nanowires, are shown to be dramatically enhanced by the judicious placement of a charge-diverting path sufficiently short to create a large phase disruption in the dominant eigenfunctions along the main path of the probability current. Phase disruption is proposed as a new general principle for the design of molecules, nanowires, and any quasi-1D quantum system with large intrinsic response and does not require charge donor-acceptors at the ends.

The Drosophila TIPE family member Sigmar interacts with the Ste20-like kinase Misshapen and modulates JNK signaling, cytoskeletal remodeling and autophagy.

TNFAIP8 and other mammalian TIPE family proteins have attracted increased interest due to their associations with disease-related processes including oncogenic transformation, metastasis, and inflammation. The molecular and cellular functions of TIPE family proteins are still not well understood. Here we report the molecular and genetic characterization of the Drosophila TNFAIP8 homolog, CG4091/sigmar.

Generalizing the correlated chromophore domain model of reversible photodegradation to include the effects of an applied electric field.

All observations of photodegradation and self-healing follow the predictions of the correlated chromophore domain model [Ramini et al., Polym. Chem.

Developing an iMALDI method.

The iMALDI (immuno-MALDI) technique involves the affinity capture of target peptides from an enzymatic digest of a sample, followed by the direct analysis of the affinity beads while on a MALDI target. For determination of peptide concentration (and, by inference, protein concentration), stable-isotope-labeled standard peptides (SIS peptides) can be added to the digest and will be captured along with the native peptides. This technique can provide the highest possible specificity by determining two molecular characteristics of the epitope-containing peptides: (1) the molecular weight, typically measured to within 100 ppm or better by MALDI-MS, and (2) the amino acid sequence, by performing MALDI-MS/MS.

Development of MRM-based assays for the absolute quantitation of plasma proteins.

Multiple reaction monitoring (MRM), sometimes called selected reaction monitoring (SRM), is a directed tandem mass spectrometric technique performed on to triple quadrupole mass spectrometers. MRM assays can be used to sensitively and specifically quantify proteins based on peptides that are specific to the target protein. Stable-isotope-labeled standard peptide analogues (SIS peptides) of target peptides are added to enzymatic digests of samples, and quantified along with the native peptides during MRM analysis.

Optomechanical dark mode.

Thermal mechanical motion hinders the use of a mechanical system in applications such as quantum information processing. Whereas the thermal motion can be overcome by cooling a mechanical oscillator to its motional ground state, an alternative approach is to exploit the use of a mechanically dark mode that can protect the system from mechanical dissipation. We have realized such a dark mode by coupling two optical modes in a silica resonator to one of its mechanical breathing modes in the regime of weak optomechanical coupling.

Interaction of cyclin-dependent kinase 12/CrkRS with cyclin K1 is required for the phosphorylation of the C-terminal domain of RNA polymerase II.

CrkRS (Cdc2-related kinase, Arg/Ser), or cyclin-dependent kinase 12 (CKD12), is a serine/threonine kinase believed to coordinate transcription and RNA splicing. While CDK12/CrkRS complexes were known to phosphorylate the C-terminal domain (CTD) of RNA polymerase II (RNA Pol II), the cyclin regulating this activity was not known. Using immunoprecipitation and mass spectrometry, we identified a 65-kDa isoform of cyclin K (cyclin K1) in endogenous CDK12/CrkRS protein complexes.

A self healing model based on polymer-mediated chromophore correlations.

Here we present a model of self healing in which correlations between chromophores, as mediated by the polymer, are key to the recovery process. Our model determines the size distribution of the correlation volume using a grand canonical ensemble through a free energy advantage parameter. Choosing a healing rate that is proportional to the number of undamaged molecules in a correlated region, and a decay rate proportional to the intensity normalized to the correlation volume, the ensemble average is shown to correctly predict decay and recovery of the population of disperse orange 11-DO11 (1-amino-2-methylanthraquinone) molecules doped in PMMA polymer as a function of time and concentration as measured with amplified spontaneous emission and linear absorption spectroscopy using only three parameters that apply to the full set of data.

The effect of pre-analytical variability on the measurement of MRM-MS-based mid- to high-abundance plasma protein biomarkers and a panel of cytokines.

Blood sample processing and handling can have a significant impact on the stability and levels of proteins measured in biomarker studies. Such pre-analytical variability needs to be well understood in the context of the different proteomics platforms available for biomarker discovery and validation. In the present study we evaluated different types of blood collection tubes including the BD P100 tube containing protease inhibitors as well as CTAD tubes, which prevent platelet activation.

Dietary patterns and ethnicity are associated with distinct plasma proteomic groups.

Background: High-abundance plasma proteins are involved in disease-associated pathways and are useful in the diagnosis of nutritional and disease states. However, little is known about how concentrations of many plasma proteins vary between individuals from different ethnocultural groups with different dietary habits.

Objective: We explored the association between plasma proteomic groups, dietary patterns, and ethnicity in the Toronto Nutrigenomics and Health Study, an ethnically diverse population of healthy young adults.

The use of multiplexed MRM for the discovery of biomarkers to differentiate iron-deficiency anemia from anemia of inflammation.

In this study we demonstrate the use of a multiplexed MRM-based assay to distinguish among normal (NL) and iron-metabolism disorder mouse models, particularly, iron-deficiency anemia (IDA), inflammation (INFL), and inflammation and anemia (INFL+IDA). Our initial panel of potential biomarkers was based on the analysis of 14 proteins expressed by candidate genes involved in iron transport and metabolism. Based on this study, we were able to identify a panel of 8 biomarker proteins: apolipoprotein A4 (APO4), transferrin, transferrin receptor 1, ceruloplasmin, haptoglobin, lactoferrin, hemopexin, and matrix metalloproteinase-8 (MMP8) that clearly distinguish among the normal and disease models.

Off-resonance and non-resonant dispersion of Kerr nonlinearity for symmetric molecules [Invited].

The exact formula is derived from the "sum over states" (SOS) quantum mechanical model for the frequency dispersion of the nonlinear refractive index coefficient n₂ for centrosymmetric molecules in the off-resonance and non-resonant regimes. This expression is characterized by interference between terms from two-photon transitions from the ground state to the even-symmetry excited states and one-photon transitions between the ground state and odd-symmetry excited states. When contributions from the two-photon terms exceed those from the one-photon terms, the non-resonant intensity-dependent refractive index n₂>0, and vice versa.

Storing optical information as a mechanical excitation in a silica optomechanical resonator.

We report the experimental demonstration of storing optical information as a mechanical excitation in a silica optomechanical resonator. We use writing and readout laser pulses tuned to one mechanical frequency below an optical cavity resonance to control the coupling between the mechanical displacement and the optical field at the cavity resonance. The writing pulse maps a signal pulse at the cavity resonance to a mechanical excitation.

The effect of electron interactions on the universal properties of systems with optimized off-resonant intrinsic hyperpolarizability.

Because of the potentially large number of important applications of nonlinear optics, researchers have expended a great deal of effort to optimize the second-order molecular nonlinear-optical response, called the hyperpolarizability. The focus of our present studies is the intrinsic hyperpolarizability, which is a scale-invariant quantity that removes the effects of simple scaling, thus being the relevant quantity for comparing molecules of varying sizes. Past theoretical studies have focused on structural properties that optimize the intrinsic hyperpolarizability, which have characterized the structure of the quantum system based on the potential energy function, placement of nuclei, geometry, and the effects of external electric and magnetic fields.

An integrated genomic, proteomic and biochemical analysis of (+)-3-carene biosynthesis in Sitka spruce (Picea sitchensis) genotypes that are resistant or susceptible to white pine weevil.

Conifers are extremely long-lived plants that have evolved complex chemical defenses in the form of oleoresin terpenoids to resist attack from pathogens and herbivores. In these species, terpenoid diversity is determined by the size and composition of the terpene synthase (TPS) gene family and the single- and multi-product profiles of these enzymes. The monoterpene (+)-3-carene is associated with resistance of Sitka spruce (Picea sitchensis) to white pine weevil (Pissodes strobi).

Identification of Leishmania-specific protein phosphorylation sites by LC-ESI-MS/MS and comparative genomics analyses.

Human pathogenic protozoa of the genus Leishmania undergo various developmental transitions during the infectious cycle that are triggered by changes in the host environment. How these parasites sense, transduce, and respond to these signals is only poorly understood. Here we used phosphoproteomic approaches to monitor signaling events in L.