Soft matter structure measurement by polarized resonant soft X-ray scattering

In many applications of soft matter, the connection between structure and performance is complex, and conventional structure measurements are not sufficient to provide a predictive structural model. Nanoscale variations in molecular orientation and composition, particularly in amorphous regions, are thought to be critical, but few techniques can probe them. I will describe our approach to polarized resonant soft X-ray scattering (P-RSoXS), which combines principles of soft X-ray spectroscopy, small-angle scattering, real-space imaging, and molecular simulation to produce a molecular scale structure measurement for soft materials and complex fluids. Progress and designs for a new P-RSoXS measurement station we are building at NIST beamlines at the National Synchrotron Light Source II will be shown. Please click Additional Files below to see the full abstract

A method for computing the overall statistical significance of a treatment effect among a group of genes

BACKGROUND: In studies that use DNA arrays to assess changes in gene expression, our goal is to evaluate the statistical significance of treatments on sets of genes. Genes can be grouped by a molecular function, a biological process, or a cellular component, e.g., gene ontology (GO) terms. The meaning of an affected GO group is often clearer than interpretations arising from a list of the statistically significant genes. RESULTS: Computer simulations demonstrated that correlations among genes invalidate many statistical methods that are commonly used to assign significance to GO terms. Ignoring these correlations overstates the statistical significance. Meta-analysis methods for combining p-values were modified to adjust for correlation. One of these methods is elaborated in the context of a comparison between two treatments. The form of the correlation adjustment depends upon the alternative hypothesis. CONCLUSION: Reliable corrections for the effect of correlations among genes on the significance level of a GO term can be constructed for an alternative hypothesis where all transcripts in the GO term increase (decrease) in response to treatment. For general alternatives, which allow some transcripts to increase and others to decrease, the bias of naïve significance calculations can be greatly decreased although not eliminated

Testing for treatment effects on gene ontology

In studies that use DNA arrays to assess changes in gene expression, it is preferable to measure the significance of treatment effects on a group of genes from a pathway or functional category such as gene ontology terms (GO terms, ) because this facilitates the interpretation of effects and may markedly increase significance. A modified meta-analysis method to combine p-values was developed to measure the significance of an overall treatment effect on such functionally-defined groups of genes, taking into account the correlation structure among genes. For hypothesis testing that allows gene expression to change in both directions, p-values are calculated under the null distribution generated by a Monte Carlo method

Designing Toxicogenomics Studies that use DNA Array Technology

Background: Bioassays are routinely used to evaluate the toxicity of test agents. Experimental designs for bioassays are largely encompassed by fixed effects linear models. In toxicogenomics studies where DNA arrays measure mRNA levels, the tissue samples are typically generated in a bioassay. These measurements introduce additional sources of variation, which must be properly managed to obtain valid tests of treatment effects.Results: An analysis of covariance model is developed which combines a fixed-effects linear model for the bioassay with important variance components associated with DNA array measurements. These models can accommodate the dominant characteristics of measurements from DNA arrays, and they account for technical variation associated with normalization, spots, dyes, and batches as well as the biological variation associated with the bioassay. An example illustrates how the model is used to identify valid designs and to compare competing designs.Conclusions: Many toxicogenomics studies are bioassays which measure gene expression using DNA arrays. These studies can be designed and analyzed using standard methods with a few modifications to account for characteristics of array measurements, such as multiple endpoints and normalization. As much as possible, technical variation associated with probes, dyes, and batches are managed by blocking treatments within these sources of variation. An example shows how some practical constraints can be accommodated by this modelling and how it allows one to objectively compare competing designs

Engineering the electrochromism and ion conduction of layer-by-layer assembled films

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2003.Includes bibliographical references.This work applies the processing technique of layer-by-layer (LBL) assembly to the creation and development of new electrochemically active materials. Elements of the thin-film electrochromic cell were chosen as a particular focus for LBL fabrication. Layer-by-layer assembly is the ideal processing tool to tailor the electrochemical systems within electrochromic cells because modulating processing conditions can greatly impact the nanoscale composition and morphology of the resultant films. For the first time, this control was used to: 1) intelligently design electrochromic LBL assembled composite films that facilitated ion motion for faster switching and exhibited enhanced or shifted coloration, 2) combine multiple electrochromic materials into novel LBL assembled composites with even higher contrast, faster switching, and multiple colored states, and finally 3) develop and optimize several LBL assembled polymer electrolyte films that display high ionic conductivity and sound mechanical integrity. Electrochromic cell elements were chosen not only for their undeveloped commercial potential, but also because they incorporate multifunctional material systems with alternative applications. Studies of LBL fabrication and the operation of electrochromic cells provide insight into intermolecular interactions, internal and external film interfaces, thin film electrochemistry, and charged species mobility in polymer solids. First investigated was the capability of LBL assembly to alter the properties of electrochromic films by varying molecular blending.(cont.) The electrochromophores for this investigation were appropriated from all corners of the materials spectrum, including discrete electrochromic polymers, conjugated polymers, soft colloidal suspensions, and inorganic particle dispersions. In each system, the influence of assembly conditions and film composition was elucidated; in particular systems the hydrophobicity, acidity, and morphology of the films were found to impact the electrochemistry and optical character of the films, providing a means to modulate these properties by directing LBL assembly design choices. Because of the high uniformity and thickness control allowed by LBL assembly, the contrast and switching performance of all LBL assembled electrochromic films were in general superior to those of films containing the same electrochromophores fabricated by other methods. One particularly promising system involved novel LBL assembled films containing the same electrochromophores fabricated by other methods. One particularly promising system involved novel LBL assembled films containing electrochromic metal hexacyanoferrate nanocrystals of the Prussian blue family. These films displayed fast and deep coloration; synthetic nanocrystal variation extended absorbance over a broad spectral range so that these inorganic/polymer composite films could potentially be considered as elements in a full-color switchable CMYK display. The power of the LBL assembly technique was leveraged further with the successful fabrication of "dual electrochrome" electrodes ...by Dean M. DeLongchamp.Ph.D

Genome-wide estimation of gender differences in the gene expression of human livers: Statistical design and analysis

BACKGROUND: Gender differences in gene expression were estimated in liver samples from 9 males and 9 females. The study tested 31,110 genes for a gender difference using a design that adjusted for sources of variation associated with cDNA arrays, normalization, hybridizations and processing conditions. RESULTS: The genes were split into 2,800 that were clearly expressed (expressed genes) and 28,310 that had expression levels in the background range (not expressed genes). The distribution of p-values from the 'not expressed' group was consistent with no gender differences. The distribution of p-values from the 'expressed' group suggested that 8 % of these genes differed by gender, but the estimated fold-changes (expression in males / expression in females) were small. The largest observed fold-change was 1.55. The 95 % confidence bounds on the estimated fold-changes were less than 1.4 fold for 79.3 %, and few (1.1%) exceed 2-fold. CONCLUSION: Observed gender differences in gene expression were small. When selecting genes with gender differences based upon their p-values, false discovery rates exceed 80 % for any set of genes, essentially making it impossible to identify any specific genes with a gender difference

Structural control of mixed ionic and electronic transport in conducting polymers.

UNLABELLED: Poly(3,4-ethylenedioxythiophene) doped with poly(styrenesulfonate), PEDOT: PSS, has been utilized for over two decades as a stable, solution-processable hole conductor. While its hole transport properties have been the subject of intense investigation, recent work has turned to PEDOT: PSS as a mixed ionic/electronic conductor in applications including bioelectronics, energy storage and management, and soft robotics. Conducting polymers can efficiently transport both holes and ions when sufficiently hydrated, however, little is known about the role of morphology on mixed conduction. Here, we show that bulk ionic and electronic mobilities are simultaneously affected by processing-induced changes in nano- and meso-scale structure in PEDOT: PSS films. We quantify domain composition, and find that domain purification on addition of dispersion co-solvents limits ion mobility, even while electronic conductivity improves. We show that an optimal morphology allows for the balanced ionic and electronic transport that is critical for prototypical mixed conductor devices. These findings may pave the way for the rational design of polymeric materials and processing routes to enhance devices reliant on mixed conduction

Material Profile Influences in Bulk-Heterojunctions

The morphology in mixed bulk-heterojunction films are compared using three different quantitative measurement techniques. We compare the vertical composition changes using high-angle annular dark-field scanning transmission electron microscopy with electron tomography and neutron and x-ray reflectometry. The three measurement techniques yield qualitatively comparable vertical concentration measurements. The presence of a metal cathode during thermal annealing is observed to alter the fullerene concentration throughout the thickness of the film for all measurements. However, the absolute vertical concentration of fullerene is quantitatively different for the three measurements. The origin of the quantitative measurement differences is discussed

Self-assembly and charge transport properties of a benzobisthiazole end-capped with dihexylthienothiophene units

The synthesis of a new conjugated material is reported; BDHTT–BBT features a central electron-deficient benzobisthiazole capped with two 3,6-dihexyl-thieno[3,2-b]thiophenes. Cyclic voltammetry was used to determine the HOMO (−5.7 eV) and LUMO (−2.9 eV) levels. The solid-state properties of the compound were investigated by X-ray diffraction on single-crystal and thin-film samples. OFETs were constructed with vacuum deposited films of BDHTT–BBT. The films displayed phase transitions over a range of temperatures and the morphology of the films affected the charge transport properties of the films. The maximum hole mobility observed from bottom-contact, top-gate devices was 3 × 10−3 cm2 V−1 s−1, with an on/off ratio of 104–105 and a threshold voltage of −42 V. The morphological and self-assembly characteristics versus electronic properties are discussed for future improvement of OFET devices

A Simple and Robust Approach to Reducing Contact Resistance in Organic Transistors

Efficient injection of charge carriers from the contacts into the semiconductor layer is crucial for achieving high-performance organic devices. The potential drop necessary to accomplish this process yields a resistance associated with the contacts, namely the contact resistance. A large contact resistance can limit the operation of devices and even lead to inaccuracies in the extraction of the device parameters. Here, we demonstrate a simple and efficient strategy for reducing the contact resistance in organic thin-film transistors by more than an order of magnitude by creating high work function domains at the surface of the injecting electrodes to promote channels of enhanced injection. We find that the method is effective for both organic small molecule and polymer semiconductors, where we achieved a contact resistance as low as 200 Ωcm and device charge carrier mobilities as high as 20 cm2V−1s−1, independent of the applied gate voltage