Variance Reduction with Array-RQMC for Tau-Leaping Simulation of Stochastic Biological and Chemical Reaction Networks

We explore the use of Array-RQMC, a randomized quasi-Monte Carlo method designed for the simulation of Markov chains, to reduce the variance when simulating stochastic biological or chemical reaction networks with $\tau$-leaping. The task is to estimate the expectation of a function of molecule copy numbers at a given future time $T$ by the sample average over $n$ sample paths, and the goal is to reduce the variance of this sample-average estimator. We find that when the method is properly applied, variance reductions by factors in the thousands can be obtained. These factors are much larger than those observed previously by other authors who tried RQMC methods for the same examples. Array-RQMC simulates an array of realizations of the Markov chain and requires a sorting function to reorder these chains according to their states, after each step. The choice of sorting function is a key ingredient for the efficiency of the method, although in our experiments, Array-RQMC was never worse than ordinary Monte Carlo, regardless of the sorting method. The expected number of reactions of each type per step also has an impact on the efficiency gain.ERDF, ESF, EXP. 2019/00432, Canada Research Chair, IVADO Research Grant, NSERC Discovery Grant RGPIN-110050

Monte Carlo and Quasi-Monte Carlo Density Estimation via Conditioning

Estimating the unknown density from which a given independent sample originates is more difficult than estimating the mean, in the sense that for the best popular non-parametric density estimators, the mean integrated square error converges more slowly than at the canonical rate of $\mathcal{O}(1/n)$. When the sample is generated from a simulation model and we have control over how this is done, we can do better. We examine an approach in which conditional Monte Carlo yields, under certain conditions, a random conditional density which is an unbiased estimator of the true density at any point. By averaging independent replications, we obtain a density estimator that converges at a faster rate than the usual ones. Moreover, combining this new type of estimator with randomized quasi-Monte Carlo to generate the samples typically brings a larger improvement on the error and convergence rate than for the usual estimators, because the new estimator is smoother as a function of the underlying uniform random numbers.IVADO Research Grant, NSERC-Canada Discorvery Grant, Canada Research Chair, Inria International Chair, ERDF, ESF, EXP. 2019/0043

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Resistivity and thermoelectric power of molten aluminium: experiment and theory

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Liquid gallium-lead spinodal calculation from effective potentials

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sequence space

Large-eddy simulation of a spatially-evolving supersonic turbulent boundary layer at M ∞ = 2

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Resistivity of the liquid gallium-lead miscibility gap system

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Liquid gallium-lead mixture phase diagram, surface tension near the critical mixing point, and prewetting transition

International audienceQuite recently, we reported a semianalytical equation of state (EOS) for the Ga-Pb alloy [Phys. Rev. B 78, 024205 (2008)], which was based on the first-order perturbation theory of fluid mixtures, within the simplified random phase approximation, in conjunction with the Grosdidier et al. model pair potentials for Ga-Ga and Pb-Pb with a suitable nonadditive pair potential between Ga-Pb unlike pairs. In the present work, we employ the present EOS to calculate the Ga-Pb phase diagram along the immiscibility gap region. The accuracy of the EOS is tested by consulting the empirical binodal curve. A statistical-mechanical-based theory for the surface tension is employed to obtain an analytical expression for the alloy surface tension. We calculated the surface tension along the bimodal curve and at extreme conditions of temperatures and pressures. The surface tension exhibits reasonably well the prewetting transition of Pb atoms at the surface of the Ga-rich liquid alloy and could qualitatively explain the prewetting phenomena occurring in the Ga-rich side of the phase diagram. The predicted prewetting line and wetting temperature qualitatively agree with the empirical measurements