Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions

Returning persons with SARS-CoV-2 to the field of play in professional golf: a risk assessment and risk reduction approach

Objectives This pilot study aimed to see whether a risk assessment and risk reduction approach was a practical and feasible approach, as compared with standard isolation for fully vaccinated, asymptomatic persons positive for SARS-CoV-2. Methods This prospective cohort study included all players and caddies participating in two large professional golf events from 7 to 20 February 2022 in South Africa. Fully vaccinated persons testing positive who were asymptomatic were subject to risk assessment and risk reduction measures to protect the integrity of the event. Asymptomatic individuals who could socially distance in outdoor areas were allowed to participate. Close contacts were subject to daily rapid antigen tests and asked to prioritise outdoor space. Results The protocols put in place for the events were practical, feasible, and well accepted by event participants and staff during the study period. There was a total of 378 player-week episodes and 378 caddie-week episodes during the study period. Three persons tested positive while registered at events during the study period (0.4% of person episodes). The positive tests were returned from two players and one caddie, all of which were asymptomatic at the time of testing. There was one high-risk contact who consistently returned negative antigen tests. There was no evidence of transmission. Conclusions The approach was practical and feasible. A risk assessment and risk reduction approach allowed fully vaccinated asymptomatic persons with SARS-CoV-2 to participate in golf, an outdoor sport where social distancing is possible, compared with standard isolation

Star Formation in the Milky Way and Nearby Galaxies

We review progress over the past decade in observations of large-scale star formation, with a focus on the interface between extragalactic and Galactic studies. Methods of measuring gas contents and star formation rates are discussed, and updated prescriptions for calculating star formation rates are provided. We review relations between star formation and gas on scales ranging from entire galaxies to individual molecular clouds.Comment: 55 pages, 15 figures, in press for Annual Reviews of Astronomy and Astrophysics; Updated with corrected equation 5, improved references, and other minor change

LEGO-II. A 3 mm molecular line study covering 100 pc of one of the most actively star-forming portions within the Milky Way disc

The current generation of (sub)mm-telescopes has allowed molecular line emission to become a major tool for studying the physical, kinematic, and chemical properties of extragalactic systems, yet exploiting these observations requires a detailed understanding of where emission lines originate within the Milky Way. In this paper, we present 60 arcsec (∼3 pc) resolution observations of many 3 mm band molecular lines across a large map of the W49 massive star-forming region (∼100 pc × 100 pc at 11 kpc), which were taken as part of the ‘LEGO’ IRAM-30m large project. We find that the spatial extent or brightness of the molecular line transitions are not well correlated with their critical densities, highlighting abundance and optical depth must be considered when estimating line emission characteristics. We explore how the total emission and emission efficiency (i.e. line brightness per H2 column density) of the line emission vary as a function of molecular hydrogen column density and dust temperature. We find that there is not a single region of this parameter space responsible for the brightest and most efficiently emitting gas for all species. For example, we find that the HCN transition shows high emission efficiency at high column density (1022 cm−2) and moderate temperatures (35 K), whilst e.g. N2H+ emits most efficiently towards lower temperatures (1022 cm−2; <20 K). We determine XCO(1−0) ∼ 0.3 × 1020 cm−2 (K km s−1) −1, and αHCN(1−0) ∼ 30 M (K km s−1 pc2) −1, which both differ significantly from the commonly adopted values. In all, these results suggest caution should be taken when interpreting molecular line emission

The Potent Respiratory System of Osedax mucofloris (Siboglinidae, Annelida) - A Prerequisite for the Origin of Bone-Eating Osedax?

Members of the conspicuous bone-eating genus, Osedax, are widely distributed on whale falls in the Pacific and Atlantic Oceans. These gutless annelids contain endosymbiotic heterotrophic bacteria in a branching root system embedded in the bones of vertebrates, whereas a trunk and anterior palps extend into the surrounding water. The unique life style within a bone environment is challenged by the high bacterial activity on, and within, the bone matrix possibly causing O2 depletion, and build-up of potentially toxic sulphide. We measured the O2 distribution around embedded Osedax and showed that the bone microenvironment is anoxic. Morphological studies showed that ventilation mechanisms in Osedax are restricted to the anterior palps, which are optimized for high O2 uptake by possessing a large surface area, large surface to volume ratio, and short diffusion distances. The blood vascular system comprises large vessels in the trunk, which facilitate an ample supply of oxygenated blood from the anterior crown to a highly vascularised root structure. Respirometry studies of O. mucofloris showed a high O2 consumption that exceeded the average O2 consumption of a broad line of resting annelids without endosymbionts. We regard this combination of features of the respiratory system of O. mucofloris as an adaptation to their unique nutrition strategy with roots embedded in anoxic bones and elevated O2 demand due to aerobic heterotrophic endosymbionts

Modeling double strand break susceptibility to interrogate structural variation in cancer

Abstract Background Structural variants (SVs) are known to play important roles in a variety of cancers, but their origins and functional consequences are still poorly understood. Many SVs are thought to emerge from errors in the repair processes following DNA double strand breaks (DSBs). Results We used experimentally quantified DSB frequencies in cell lines with matched chromatin and sequence features to derive the first quantitative genome-wide models of DSB susceptibility. These models are accurate and provide novel insights into the mutational mechanisms generating DSBs. Models trained in one cell type can be successfully applied to others, but a substantial proportion of DSBs appear to reflect cell type-specific processes. Using model predictions as a proxy for susceptibility to DSBs in tumors, many SV-enriched regions appear to be poorly explained by selectively neutral mutational bias alone. A substantial number of these regions show unexpectedly high SV breakpoint frequencies given their predicted susceptibility to mutation and are therefore credible targets of positive selection in tumors. These putatively positively selected SV hotspots are enriched for genes previously shown to be oncogenic. In contrast, several hundred regions across the genome show unexpectedly low levels of SVs, given their relatively high susceptibility to mutation. These novel coldspot regions appear to be subject to purifying selection in tumors and are enriched for active promoters and enhancers. Conclusions We conclude that models of DSB susceptibility offer a rigorous approach to the inference of SVs putatively subject to selection in tumors

Social Algorithms

This article concerns the review of a special class of swarm intelligence based algorithms for solving optimization problems and these algorithms can be referred to as social algorithms. Social algorithms use multiple agents and the social interactions to design rules for algorithms so as to mimic certain successful characteristics of the social/biological systems such as ants, bees, bats, birds and animals.Comment: Encyclopedia of Complexity and Systems Science, 201

Gorab is a Golgi protein required for structure and duplication of Drosophila centrioles.

We demonstrate that a Drosophila Golgi protein, Gorab, is present not only in the trans-Golgi but also in the centriole cartwheel where, complexed to Sas6, it is required for centriole duplication. In addition to centriole defects, flies lacking Gorab are uncoordinated due to defects in sensory cilia, which lose their nine-fold symmetry. We demonstrate the separation of centriole and Golgi functions of Drosophila Gorab in two ways: first, we have created Gorab variants that are unable to localize to trans-Golgi but can still rescue the centriole and cilia defects of gorab null flies; second, we show that expression of C-terminally tagged Gorab disrupts Golgi functions in cytokinesis of male meiosis, a dominant phenotype overcome by mutations preventing Golgi targeting. Our findings suggest that during animal evolution, a Golgi protein has arisen with a second, apparently independent, role in centriole duplication.D.M.G. is grateful for a Wellcome Investigator Award, which supported this work. The study was initiated with support from Cancer Research UK

Targeting transcription regulation in cancer with a covalent CDK7 inhibitor

Tumour oncogenes include transcription factors that co-opt the general transcriptional machinery to sustain the oncogenic state, but direct pharmacological inhibition of transcription factors has so far proven difficult. However, the transcriptional machinery contains various enzymatic cofactors that can be targeted for the development of new therapeutic candidates, including cyclin-dependent kinases (CDKs). Here we present the discovery and characterization of a covalent CDK7 inhibitor, THZ1, which has the unprecedented ability to target a remote cysteine residue located outside of the canonical kinase domain, providing an unanticipated means of achieving selectivity for CDK7. Cancer cell-line profiling indicates that a subset of cancer cell lines, including human T-cell acute lymphoblastic leukaemia (T-ALL), have exceptional sensitivity to THZ1. Genome-wide analysis in Jurkat T-ALL cells shows that THZ1 disproportionally affects transcription of RUNX1 and suggests that sensitivity to THZ1 may be due to vulnerability conferred by the RUNX1 super-enhancer and the key role of RUNX1 in the core transcriptional regulatory circuitry of these tumour cells. Pharmacological modulation of CDK7 kinase activity may thus provide an approach to identify and treat tumour types that are dependent on transcription for maintenance of the oncogenic state.National Institutes of Health (U.S.) (Grant HG002668)National Institutes of Health (U.S.) (Grant CA109901