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Bowdoin Orient, v. 11, no. 4
Date: 1881-06-08
Access: Open access
- includes frontmatter; "Ivy Number" issue
Benchmarking Ab Initio Computational Methods for the Quantitative Prediction of Sunlight-Driven Pollutant Degradation in Aquatic Environments
Date: 2016-05-01
Creator: Kasidet Trerayapiwat
Access: Open access
- Understanding the changes in molecular electronic structure following the absorption of light is a fundamental challenge for the goal of predicting photochemical rates and mechanisms. Proposed here is a systematic benchmarking method to evaluate accuracy of a model to quantitatively predict photo-degradation of small organic molecules in aquatic environments. An overview of underlying com- putational theories relevant to understanding sunlight-driven electronic processes in organic pollutants is presented. To evaluate the optimum size of solvent sphere, molecular Dynamics and Time Dependent Density Functional Theory (MD-TD-DFT) calculations of an aniline molecule in di↵erent numbers of water molecules using CAM-B3LYP functional yielded excited state energy and oscillator strength values, which were compared with data from experimental absorption spectra. For the first time, a statistical method of comparing experimental and theoretical data is proposed. Underlying Gaussian functions of absorption spectra were deconvoluted and integrated to calculate experimental oscillator strengths. A Matlab code written by Soren Eustis was utilized to decluster MD-TD-DFT results. The model with 256 water molecules was decided to give the most accurate results with optimized com- putational cost and accuracy. MD-TD-DFT calculations were then performed on aniline, 3-F-aniline, 4-F-aniline, 3-Cl-aniline, 4-MeOacetophenone, and (1,3)-dimethoxybenzophenone with CAM-B3LYP, PBE0, M06-2X, LCBLYP, and BP86 functionals. BP86 functional was determined to be the best functional. Github repository: https://github.com/eustislab/MD_Scripts
Captured segment exchange: A strategy for custom engineering large genomic regions in Drosophila melanogaster
Date: 2013-04-24
Creator: Jack R. Bateman, Michael F. Palopoli, Sarah T. Dale, Jennifer E. Stauffer, Anita L., Shah, Justine E. Johnson, Conor W. Walsh, Hanna Flaten, Christine M. Parsons
Access: Open access
- Site-specific recombinases (SSRs) are valuable tools for manipulating genomes. In Drosophila, thousands of transgenic insertions carrying SSR recognition sites have been distributed throughout the genome by several large-scale projects. Here we describe a method with the potential to use these insertions to make custom alterations to the Drosophila genome in vivo. Specifically, by employing recombineering techniques and a dual recombinase-mediated cassette exchange strategy based on the phiC31 integrase and FLP recombinase, we show that a large genomic segment that lies between two SSR recognition-site insertions can be "captured" as a target cassette and exchanged for a sequence that was engineered in bacterial cells. We demonstrate this approach by targeting a 50-kb segment spanning the tsh gene, replacing the existing segment with corresponding recombineered sequences through simple and efficient manipulations. Given the high density of SSR recognition-site insertions in Drosophila, our method affords a straightforward and highly efficient approach to explore gene function in situ for a substantial portion of the Drosophila genome. © 2013 by the Genetics Society of America.