Understanding the reactivity of molecular precursors to colloidal nanocrystals

Colloidal semiconductor nanocrystals are materials with intriguing properties that make them useful for a diverse array of applications such as photocatalysts, light-absorbing materials in solar cells, light emitting diodes and luminescent biological tags, to name only a few. Performance of nanomaterials in these applications is directly related to the size, shape and stoichiometry of the nanocrystals. Strategies exist to control these characteristics during colloidal synthesis, but they tend to rely on certain surfactants, additives, or multi-step procedures to achieve desirable properties. This thesis describes new directions in the synthesis of colloidal nanomaterials that use computational chemistry as a guide. Using new and efficient methods in density functional theory (DFT) to reliably calculate bond dissociation energies (BDEs) of organodichalcogenide (sulfide or selenide) precursors enables the rational synthesis of dot, rod and tetrapod morphology cadmium chalcogenide nanocrystals. Precursors with weaker C-E (E = S, Se) bonds and stronger E-E bonds yielded dot-shaped nanocrystals, while precursors with stronger C-E and weaker E-E bonds afforded rod or tetrapod shapes. This methodology readily extends to the BDE calculation of tertiary phosphine chalcogenides with substituted phenyl, alkyl, perfluoroalkyl moieties or Verkade-type cage structures. In these systems the BDE of a series of P--S or P--Se bonds increases with slightly increasing bond distance, although the BDE of P--Se bonds is significantly lower than P--S bonds. Another promising method in colloidal nanocrystal synthesis is photochemical decomposition of precursors to access unusual phases or shapes. This thesis also describes the photochemical synthesis of cobalt(III) oxyhydroxide, Co(O)OH, nanocrystals from chloropentaamminecobalt(III) salts in aqueous solution. Compared to the thermal decomposition of the starting material in the absence of light, the photochemically-synthesized material exhibits a smaller size with a lower-temperature phase transition to cobalt(II,III) oxide, Co3O4

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

A global metagenomic map of urban microbiomes and antimicrobial resistance

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.Funding: the Tri-I Program in Computational Biology and Medicine (CBM) funded by NIH grant 1T32GM083937; GitHub; Philip Blood and the Extreme Science and Engineering Discovery Environment (XSEDE), supported by NSF grant number ACI-1548562 and NSF award number ACI-1445606; NASA (NNX14AH50G, NNX17AB26G), the NIH (R01AI151059, R25EB020393, R21AI129851, R35GM138152, U01DA053941); STARR Foundation (I13- 0052); LLS (MCL7001-18, LLS 9238-16, LLS-MCL7001-18); the NSF (1840275); the Bill and Melinda Gates Foundation (OPP1151054); the Alfred P. Sloan Foundation (G-2015-13964); Swiss National Science Foundation grant number 407540_167331; NIH award number UL1TR000457; the US Department of Energy Joint Genome Institute under contract number DE-AC02-05CH11231; the National Energy Research Scientific Computing Center, supported by the Office of Science of the US Department of Energy; Stockholm Health Authority grant SLL 20160933; the Institut Pasteur Korea; an NRF Korea grant (NRF-2014K1A4A7A01074645, 2017M3A9G6068246); the CONICYT Fondecyt Iniciación grants 11140666 and 11160905; Keio University Funds for Individual Research; funds from the Yamagata prefectural government and the city of Tsuruoka; JSPS KAKENHI grant number 20K10436; the bilateral AT-UA collaboration fund (WTZ:UA 02/2019; Ministry of Education and Science of Ukraine, UA:M/84-2019, M/126-2020); Kyiv Academic Univeristy; Ministry of Education and Science of Ukraine project numbers 0118U100290 and 0120U101734; Centro de Excelencia Severo Ochoa 2013–2017; the CERCA Programme / Generalitat de Catalunya; the CRG-Novartis-Africa mobility program 2016; research funds from National Cheng Kung University and the Ministry of Science and Technology; Taiwan (MOST grant number 106-2321-B-006-016); we thank all the volunteers who made sampling NYC possible, Minciencias (project no. 639677758300), CNPq (EDN - 309973/2015-5), the Open Research Fund of Key Laboratory of Advanced Theory and Application in Statistics and Data Science – MOE, ECNU, the Research Grants Council of Hong Kong through project 11215017, National Key RD Project of China (2018YFE0201603), and Shanghai Municipal Science and Technology Major Project (2017SHZDZX01) (L.S.