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

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Low hole polaron migration barrier in lithium peroxide

We present computational evidence of polaronic hole trapping and migration in lithium peroxide (Li[subscript 2]O[subscript 2]), a material of interest in lithium-air batteries. We find that the hole forms in the π* antibonding molecular orbitals of the peroxide (O2[superscript 2−]) anion, and that this trapped hole induces significant local lattice distortion, forming a polaron. Our study finds migration barriers for the free polaron to be between 68 and 152 meV, depending on the hopping direction. This low barrier suggests that this material might not be as insulating as previously assumed, provided that the formation of carriers can be achieved. One transport limitation may arise from lithium vacancies, which we find to strongly bind to the polaron. This result, in combination with previous experimental results, suggests that electronic conductivity in this material is likely to be determined by vacancy diffusion.United States. Dept. of Energy (contract DE-FG02-96ER45571)Massachusetts Institute of Technology. Ford-MIT Alliance programUnited States. Dept. of Energy. Batteries for Advanced Transportation Technologies (BATT) program (contract DE-AC02-05CH11231

First-principles study of the oxygen evolution reaction of lithium peroxide in the lithium-air battery

The lithium-air chemistry is an interesting candidate for the next-generation batteries with high specific energy. However, this new battery technology is facing substantial challenges, such as a high overpotential upon charging, poor reversibility, and low power density. Using first-principles calculations, we study the oxygen evolution reaction (OER) on the low-index surfaces of lithium peroxide. The elementary reaction steps and the energy profile of the OER are identified on the low-index surfaces of lithium peroxide. We find that the OER processes are kinetically limited by the high energy barrier for the evolution of oxygen molecules and that the rate of the OER processes is highly dependent on the surface orientation.Ford Motor Company (Ford-MIT Alliance program

SI2-SSI: Collaborative Research: A Robust High-throughput Ab initio Computation and Analysis Software Framework for Interface Materials Science

<div>A three-year SI2-SSI project is proposed to develop an open-source Ab initio Interface Materials Computation and Analysis in Python (aimcapy) software framework for data-driven interface materials science. This framework will be built on the existing pymatgen, pymatgen-db, custodian and FireWorks software libraries, integrating them into a complete, user-friendly, and flexible system for high-throughput (HT) ab initio computations and analysis. This SSI will greatly expand the capabilities of this framework beyond ground state bulk electronic structure and energy calculations, targeting developmental efforts on three key focus areas of great interest to interface materials science: (i) Ab-initio thermodynamics of surfaces and interfaces; ii) Advanced methods for materials kinetics and diffusion at materials interfaces; and iii) Automated algorithms for structural construction of grain boundary and post data-processing and analysis. Ultimately, to expand its usage to various research areas, the proposed aimcapy software framework will be designed to interface with any energy evaluation engines (ab initio and force-field-based classical mechanics codes) with minimal changes of the source.</div

First Principles Study of the Li₁₀GeP₂S₁₂ Lithium Super Ionic Conductor Material

First Principles Study of the Li₁₀GeP₂S₁₂ Lithium Super Ionic Conductor Materia

Nanoscale Stabilization of Sodium Oxides: Implications for Na–O₂ Batteries

The thermodynamic stability of materials can depend on particle size due to the competition between surface and bulk energy. In this Letter, we show that, while sodium peroxide (Na₂O₂) is the stable bulk phase of Na in an oxygen environment at standard conditions, sodium superoxide (NaO₂) is considerably more stable at the nanoscale. As a consequence, the superoxide requires a much lower nucleation energy than the peroxide, explaining why it can be observed as the discharge product in some Na–O₂ batteries. As the superoxide can be recharged (decomposed) at much lower overpotentials than the peroxide, these findings are important to create highly reversible Na–O₂ batteries. We derive the specific electrochemical conditions to nucleate and retain Na-superoxides and comment on the importance of considering the nanophase thermodynamics when optimizing an electrochemical system

A Facile Mechanism for Recharging Li₂O₂ in Li–O₂ Batteries

Li–air is a novel battery technology with the potential to offer very high specific energy, but which currently suffers from a large charging overpotential and low power density. In this work, we use ab initio calculations to demonstrate that a facile mechanism for recharging Li₂O₂ exists. Rather than the direct decomposition pathway of Li₂O₂ into Li and O₂ suggested by equilibrium thermodynamics, we find an alternative reaction pathway based on topotactic delithiation of Li₂O₂ to form off-stoichiometric Li_2–<i>x</i>O₂ compounds akin to the charging mechanism in typical Li-ion intercalation electrodes. The low formation energy of bulk Li_2–<i>x</i>O₂ phases confirms that this topotactic delithiation mechanism is rendered accessible at relatively small overpotentials of ∼0.3–0.4 V and is likely to be kinetically favored over Li₂O₂ decomposition. Our findings indicate that at the Li₂O₂ particle level there are no obstacles to increase the current density, and point to an exciting opportunity to create fast charging Li–air systems

Just Accepted Manuscript •

Abstract In this work, we investigated the effect of Rb and Ta doping on the ionic conductivity and stability of the garnet Li 7+2x-y (La 3-x Rb x )(Zr 2-y Ta y )O 12 (0≤x≤0.375, 0≤y≤1) superionic conductor using first principles calculations. Our results indicate that doping does not greatly alter the topology of the migration pathway, but instead acts primarily to change the lithium concentration. The structure with the lowest activation energy and highest room temperature conductivity is Li 6.75 , has a lower activation energy than c-LLZO, but further Rb doping leads to a dramatic decrease in performance. We also examined the effect of changing the lattice parameter at fixed lithium concentration and found that a decrease in the lattice parameter leads to a rapid decline in Li + conductivity, whereas an expanded lattice offers only marginal improvement. This result suggests that doping with larger cations will not provide a significant enhancement in performance. Our result