The Selection of Thermometers for General Organic Chemistry

In selecting suitable thermometers for the use of students in General Organic Chemistry, it is often found that the ordinary chemical thermometers on the market at moderate prices have a number of defects. Some of these are as follows: 1. Graduation lines too close together, making reading difficult. 2. Lack of sufficient accuracy. 3. Stems too large, causing difficulty when more than one hole must be bored through a small cork

A Convenient Method for the Laboratoy Preparation of Absolute Ethyl Alcohol

The rates of dehydration of ethyl alcohol of 95 per cent strength by calcium oxide were determined at 15°, 45°, and 78°. By two successive treatments for two months each with lime at room temperature, the alcohol was found to be dehydrated in a satisfactory manner. The same result was found to be accomplished at 45° by two treatments of one week each. In neither case is refluxing necessary

Correlation Functions for Diffusion-Limited Annihilation, A + A -> 0

The full hierarchy of multiple-point correlation functions for diffusion-limited annihilation, A + A -> 0, is obtained analytically and explicitly, following the method of intervals. In the long time asymptotic limit, the correlation functions of annihilation are identical to those of coalescence, A + A -> A, despite differences between the two models in other statistical measures, such as the interparticle distribution function

A pedestrian's view on interacting particle systems, KPZ universality, and random matrices

These notes are based on lectures delivered by the authors at a Langeoog seminar of SFB/TR12 "Symmetries and universality in mesoscopic systems" to a mixed audience of mathematicians and theoretical physicists. After a brief outline of the basic physical concepts of equilibrium and nonequilibrium states, the one-dimensional simple exclusion process is introduced as a paradigmatic nonequilibrium interacting particle system. The stationary measure on the ring is derived and the idea of the hydrodynamic limit is sketched. We then introduce the phenomenological Kardar-Parisi-Zhang (KPZ) equation and explain the associated universality conjecture for surface fluctuations in growth models. This is followed by a detailed exposition of a seminal paper of Johansson that relates the current fluctuations of the totally asymmetric simple exclusion process (TASEP) to the Tracy-Widom distribution of random matrix theory. The implications of this result are discussed within the framework of the KPZ conjecture.Comment: 52 pages, 4 figures; to appear in J. Phys. A: Math. Theo

Nonlinear reactive systems viewed as Boolean dynamical systems

We present a stochastic, time-discrete boolean model which mimics the mesoscopic dynamics of the desorption reactions $A+A\to A+S$ and $A+A\to S+S$ in a 1D lattice. In the continuous-time limit, we derive a hierarchy of dynamical equations for the subset of moments involving contiguous lattice sites. The solution of the hierarchy allows to compute the exact dynamics of the mean coverage for both microscopic and coarse-grained initial conditions, which turn out to be different from the mean field predictions. The evolution equations for the mean coverage and the second order moments are shown to be equivalent to those provided by a time-continuous Master equation. The important role of higher order fluctuations is brought out by the failure of a truncation scheme retaining only two-particle fluctuation correlations.Comment: 30 pages, 9 figure

Structural genomics is the largest contributor of novel structural leverage

The Protein Structural Initiative (PSI) at the US National Institutes of Health (NIH) is funding four large-scale centers for structural genomics (SG). These centers systematically target many large families without structural coverage, as well as very large families with inadequate structural coverage. Here, we report a few simple metrics that demonstrate how successfully these efforts optimize structural coverage: while the PSI-2 (2005-now) contributed more than 8% of all structures deposited into the PDB, it contributed over 20% of all novel structures (i.e. structures for protein sequences with no structural representative in the PDB on the date of deposition). The structural coverage of the protein universe represented by today’s UniProt (v12.8) has increased linearly from 1992 to 2008; structural genomics has contributed significantly to the maintenance of this growth rate. Success in increasing novel leverage (defined in Liu et al. in Nat Biotechnol 25:849–851, 2007) has resulted from systematic targeting of large families. PSI’s per structure contribution to novel leverage was over 4-fold higher than that for non-PSI structural biology efforts during the past 8 years. If the success of the PSI continues, it may just take another ~15 years to cover most sequences in the current UniProt database

The Year of Polar Prediction

The Year of Polar Prediction (YOPP) has the mission to enable a significant improvement in environmental prediction capabilities for the polar regions and beyond, by coordinating a period of intensive observing, modelling, prediction, verification, user- engagement and education activities. The YOPP Core Phase will be from mid-2017 to mid-2019, flanked by a Preparation Phase and a Consolidation Phase. YOPP is a key component of the World Meteorological Organization – World Weather Research Programme (WMO-WWRP) Polar Prediction Project (PPP). The objectives of YOPP are to: 1. Improve the existing polar observing system (better coverage, higher-quality observations); 2. Gather additional observations through field programmes aimed at improving understanding of key polar processes; 3. Develop improved representation of key polar processes in coupled (and uncoupled) models used for prediction; 4. Develop improved (coupled) data assimilation systems accounting for challenges in the polar regions such as sparseness of observational data; 5. Explore the predictability of the atmosphere-cryosphere-ocean system, with a focus on sea ice, on time scales from days to seasons; 6. Improve understanding of linkages between polar regions and lower latitudes and assess skill of models representing these linkages; 7. Improve verification of polar weather and environmental predictions to obtain better quantitative knowledge on model performance, and on the skill, especially for user-relevant parameters; 8. Demonstrate the benefits of using predictive information for a spectrum of user types and services; 9. Provide training opportunities to generate a sound knowledge base (and its transfer across generations) on polar prediction related issues. The PPP Steering Group provides endorsement for projects that contribute to YOPP to enhance coordination, visibility, communication, and networking. This White Paper is based largely on the much more comprehensive YOPP Implementation Plan (WWRP/PPP No. 3 – 2014), but has an emphasis on Arctic observations

Adaptations to Submarine Hydrothermal Environments Exemplified by the Genome of Nautilia profundicola

Submarine hydrothermal vents are model systems for the Archaean Earth environment, and some sites maintain conditions that may have favored the formation and evolution of cellular life. Vents are typified by rapid fluctuations in temperature and redox potential that impose a strong selective pressure on resident microbial communities. Nautilia profundicola strain Am-H is a moderately thermophilic, deeply-branching Epsilonproteobacterium found free-living at hydrothermal vents and is a member of the microbial mass on the dorsal surface of vent polychaete, Alvinella pompejana. Analysis of the 1.7-Mbp genome of N. profundicola uncovered adaptations to the vent environment—some unique and some shared with other Epsilonproteobacterial genomes. The major findings included: (1) a diverse suite of hydrogenases coupled to a relatively simple electron transport chain, (2) numerous stress response systems, (3) a novel predicted nitrate assimilation pathway with hydroxylamine as a key intermediate, and (4) a gene (rgy) encoding the hallmark protein for hyperthermophilic growth, reverse gyrase. Additional experiments indicated that expression of rgy in strain Am-H was induced over 100-fold with a 20°C increase above the optimal growth temperature of this bacterium and that closely related rgy genes are present and expressed in bacterial communities residing in geographically distinct thermophilic environments. N. profundicola, therefore, is a model Epsilonproteobacterium that contains all the genes necessary for life in the extreme conditions widely believed to reflect those in the Archaean biosphere—anaerobic, sulfur, H2- and CO2-rich, with fluctuating redox potentials and temperatures. In addition, reverse gyrase appears to be an important and common adaptation for mesophiles and moderate thermophiles that inhabit ecological niches characterized by rapid and frequent temperature fluctuations and, as such, can no longer be considered a unique feature of hyperthermophiles

Recurrent SARS-CoV-2 mutations in immunodeficient patients

Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunodeficient patients are an important source of variation for the virus but are understudied. Many case studies have been published which describe one or a small number of long-term infected individuals but no study has combined these sequences into a cohesive dataset. This work aims to rectify this and study the genomics of this patient group through a combination of literature searches as well as identifying new case series directly from the COVID-19 Genomics UK (COG-UK) dataset. The spike gene receptor-binding domain and N-terminal domain (NTD) were identified as mutation hotspots. Numerous mutations associated with variants of concern were observed to emerge recurrently. Additionally a mutation in the envelope gene, T30I was determined to be the second most frequent recurrently occurring mutation arising in persistent infections. A high proportion of recurrent mutations in immunodeficient individuals are associated with ACE2 affinity, immune escape, or viral packaging optimisation.There is an apparent selective pressure for mutations that aid cell–cell transmission within the host or persistence which are often different from mutations that aid inter-host transmission, although the fact that multiple recurrent de novo mutations are considered defining for variants of concern strongly indicates that this potential source of novel variants should not be discounted

The Year of Polar Prediction in the Southern Hemisphere (YOPP-SH)

The Year of Polar Prediction in the Southern Hemisphere (YOPP-SH) had a Special Observing Period (SOP) that ran from November 16, 2018 to February 15, 2019, a period chosen to span the austral warm season months of greatest operational activity in the Antarctic. Some 2200 additional radiosondes were launched during the 3-month SOP, roughly doubling the routine program, and the network of drifting buoys in the Southern Ocean was enhanced. An evaluation of global model forecasts during the SOP and using its data has confirmed that extratropical Southern Hemisphere forecast skill lags behind that in the Northern Hemisphere with the contrast being greatest between the southern and northern polar regions. Reflecting the application of the SOP data, early results from observing system experiments show that the additional radiosondes