Well-resolved measurements of the small-scale dissipation statistics within turbulent channel flow are reported for a range of Reynolds numbers from $Re_{{\it\tau}}\approx 500$ to 4000. In this flow, the local large-scale Reynolds number based on the longitudinal integral length scale is found to poorly describe the Reynolds number dependence of the small-scale statistics. When a length scale based on Townsend’s attached-eddy hypothesis is used to define the local large-scale Reynolds number, the Reynolds number scaling behaviour was found to be more consistent with that observed in homogeneous, isotropic turbulence. The Reynolds number scaling of the dissipation moments up to the sixth moment was examined and the results were found to be in good agreement with predicted scaling behaviour (Schumacher et al. , Proc. Natl Acad. Sci. USA , vol. 111, 2014, pp. 10961–10965). The probability density functions of the local dissipation scales (Yakhot, Physica D, vol. 215 (2), 2006, pp. 166–174) were also determined and, when the revised local large-scale Reynolds number is used for normalization, provide support for the existence of a universal distribution which scales differently for inner and outer regions.
more »
« less
Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph
Genome wide optical maps are high resolution restriction maps that give a unique numeric representation to a genome. They are produced by assembling hundreds of thousands of single molecule optical maps, which are called Rmaps. Unfortunately, there are very few choices for assembling Rmap data. There exists only one publicly-available non-proprietary method for assembly and one proprietary software that is available via an executable. Furthermore, the publicly-available method, by Valouev et al. (Proc Natl Acad Sci USA 103(43):15770–15775, 2006), follows the overlap-layout-consensus (OLC) paradigm, and therefore, is unable to scale for relatively large genomes. The algorithm behind the proprietary method, Bionano Genomics’ Solve, is largely unknown. In this paper, we extend the definition of bi-labels in the paired de Bruijn graph to the context of optical mapping data, and present the first de Bruijn graph based method for Rmap assembly. We implement our approach, which we refer to as
- PAR ID:
- 10230865
- Publisher / Repository:
- Springer Science + Business Media
- Date Published:
- Journal Name:
- Algorithms for Molecular Biology
- Volume:
- 16
- Issue:
- 1
- ISSN:
- 1748-7188
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
null (Ed.)From the famous 1918 H1N1 influenza to the present COVID-19 pandemic, the need for improved viral detection techniques is all too apparent. The aim of the present paper is to show that identification of individual virus particles in clinical sample materials quickly and reliably is near at hand. First of all, our team has developed techniques for identification of virions based on a modular atomic force microscopy (AFM). Furthermore, femtosecond adaptive spectroscopic techniques with enhanced resolution via coherent anti-Stokes Raman scattering (FASTER CARS) using tip-enhanced techniques markedly improves the sensitivity [M. O. Scully, et al ., Proc. Natl. Acad. Sci. U.S.A. 99, 10994–11001 (2002)].more » « less
-
Stochastic and a posteriori optimization to mitigate coil manufacturing errors in stellarator designAbstract It was recently shown in Wechsung et al (2022 Proc. Natl Acad. Sci. USA 119 e2202084119) that there exist electromagnetic coils that generate magnetic fields, which are excellent approximations to quasi-symmetric fields and have very good particle confinement properties. Using a Gaussian process-based model for coil perturbations, we investigate the impact of manufacturing errors on the performance of these coils. We show that even fairly small errors result in noticeable performance degradation. While stochastic optimization yields minor improvements, it is not possible to mitigate these errors significantly. As an alternative to stochastic optimization, we then formulate a new optimization problem for computing optimal adjustments of the coil positions and currents without changing the shapes of the coil. These a-posteriori adjustments are able to reduce the impact of coil errors by an order of magnitude, providing a new perspective for dealing with manufacturing tolerances in stellarator design.more » « less
-
In less than 25 y, the field of animal genome science has transformed from a discipline seeking its first glimpses into genome sequences across the Tree of Life to a global enterprise with ambitions to sequence genomes for all of Earth’s eukaryotic diversity [H. A. Lewin et al. , Proc. Natl. Acad. Sci. U.S.A. 115, 4325–4333 (2018)]. As the field rapidly moves forward, it is important to take stock of the progress that has been made to best inform the discipline’s future. In this Perspective, we provide a contemporary, quantitative overview of animal genome sequencing. We identified the best available genome assemblies in GenBank, the world’s most extensive genetic database, for 3,278 unique animal species across 24 phyla. We assessed taxonomic representation, assembly quality, and annotation status for major clades. We show that while tremendous taxonomic progress has occurred, stark disparities in genomic representation exist, highlighted by a systemic overrepresentation of vertebrates and underrepresentation of arthropods. In terms of assembly quality, long-read sequencing has dramatically improved contiguity, whereas gene annotations are available for just 34.3% of taxa. Furthermore, we show that animal genome science has diversified in recent years with an ever-expanding pool of researchers participating. However, the field still appears to be dominated by institutions in the Global North, which have been listed as the submitting institution for 77% of all assemblies. We conclude by offering recommendations for improving genomic resource availability and research value while also broadening global representation.more » « less
-
Understanding the role of nonequilibrium driving in self-organization is crucial for developing a predictive description of biological systems, yet it is impeded by their complexity. The actin cytoskeleton serves as a paradigm for how equilibrium and nonequilibrium forces combine to give rise to self-organization. Motivated by recent experiments that show that actin filament growth rates can tune the morphology of a growing actin bundle cross-linked by two competing types of actin-binding proteins [S. L. Freedman et al. , Proc. Natl. Acad. Sci. U.S.A. 116, 16192–16197 (2019)], we construct a minimal model for such a system and show that the dynamics of a growing actin bundle are subject to a set of thermodynamic constraints that relate its nonequilibrium driving, morphology, and molecular fluxes. The thermodynamic constraints reveal the importance of correlations between these molecular fluxes and offer a route to estimating microscopic driving forces from microscopy experiments.more » « less
