Numerical dissipation vs. subgrid-scale modelling for large eddy simulation

This study presents an alternative way to perform large eddy simulation based on a targeted numerical dissipation introduced by the discretization of the viscous term. It is shown that this regularisation technique is equivalent to the use of spectral vanishing viscosity. The flexibility of the method ensures high-order accuracy while controlling the level and spectral features of this purely numerical viscosity. A Pao-like spectral closure based on physical arguments is used to scale this numerical viscosity a priori. It is shown that this way of approaching large eddy simulation is more efficient and accurate than the use of the very popular Smagorinsky model in standard as well as in dynamic version. The main strength of being able to correctly calibrate numerical dissipation is the possibility to regularise the solution at the mesh scale. Thanks to this property, it is shown that the solution can be seen as numerically converged. Conversely, the two versions of the Smagorinsky model are found unable to ensure regularisation while showing a strong sensitivity to numerical errors. The originality of the present approach is that it can be viewed as implicit large eddy simulation, in the sense that the numerical error is the source of artificial dissipation, but also as explicit subgrid-scale modelling, because of the equivalence with spectral viscosity prescribed on a physical basis

Physical scaling of numerical dissipation for LES

In this work, we are interested in an alternative way to perform LES using a numerical substitute of a subgrid-scale model with a calibration based on physical inputs

Xcompact3D: An open-source framework for solving turbulence problems on a Cartesian mesh

Xcompact3D is a Fortran 90–95 open-source framework designed for fast and accurate simulations of turbulent flows, targeting CPU-based supercomputers. It is an evolution of the flow solver Incompact3D which was initially designed in France in the mid-90’s for serial processors to solve the incompressible Navier–Stokes equations. Incompact3D was then ported to parallel High Performance Computing (HPC) systems in the early 2010’s. Very recently the capabilities of Incompact3D have been extended so that it can now tackle more flow regimes (from incompressible flows to compressible flows at low Mach numbers), resulting in the design of a new user-friendly framework called Xcompact3D. The present manuscript presents an overview of Xcompact3D with a particular focus on its functionalities, its ready-to-run simulations and a few case studies to demonstrate its impact

Cortical gyrification in relation to age and cognition in older adults

Gyrification of the cerebral cortex changes with aging and relates to development of cognitive function during early life and midlife. Little is known about how gyrification relates to age and cognitive function later in life. We investigated this in 4397 individuals (mean age: 63.5 years, range: 45.7 to 97.9) from the Rotterdam Study, a population-based cohort. Global and local gyrification were assessed from T1-weighted images. A measure for global cognition, the g-factor, was calculated from five cognitive tests. Older age was associated with lower gyrification (mean difference per year ​= ​−0.0021; 95% confidence interval ​= ​−0.0025; −0.0017). Non-linear terms did not improve the models. Age related to lower gyrification in the parietal, frontal, temporal and occipital regions, and higher gyrification in the medial prefrontal cortex. Higher levels of the g-factor were associated with higher global gyrification (mean difference per g-factor unit ​= ​0.0044; 95% confidence interval ​= ​0.0015; 0.0073). Age and the g-factor did not interact in relation to gyrification (p ​> ​0.05). The g-factor bilaterally associated with gyrification in three distinct clusters. The first cluster encompassed the superior temporal gyrus, the insular cortex and the postcentral gyrus, the second cluster the lingual gyrus and the precuneus, and the third cluster the orbitofrontal cortex. These clusters largely remained statistically significant after correction for cortical surface area. Overall, the results support the notion that gyrification varies with aging and cognition during and after midlife, and suggest that gyrification is a potential marker for age-related brain and co

One-Point Probability Distribution Functions of Supersonic Turbulent Flows in Self-Gravitating Media

Turbulence is essential for understanding the structure and dynamics of molecular clouds and star-forming regions. There is a need for adequate tools to describe and characterize the properties of turbulent flows. One-point probability distribution functions (pdf's) of dynamical variables have been suggested as appropriate statistical measures and applied to several observed molecular clouds. However, the interpretation of these data requires comparison with numerical simulations. To address this issue, SPH simulations of driven and decaying, supersonic, turbulent flows with and without self-gravity are presented. In addition, random Gaussian velocity fields are analyzed to estimate the influence of variance effects. To characterize the flow properties, the pdf's of the density, of the line-of-sight velocity centroids, and of the line centroid increments are studied. This is supplemented by a discussion of the dispersion and the kurtosis of the increment pdf's, as well as the spatial distribution of velocity increments for small spatial lags. From the comparison between different models of interstellar turbulence, it follows that the inclusion of self-gravity leads to better agreement with the observed pdf's in molecular clouds. The increment pdf's for small spatial lags become exponential for all considered velocities. However, all the processes considered here lead to non-Gaussian signatures, differences are only gradual, and the analyzed pdf's are in addition projection dependent. It appears therefore very difficult to distinguish between different physical processes on the basis of pdf's only, which limits their applicability for adequately characterizing interstellar turbulence.Comment: 38 pages (incl. 17 figures), accepted for publication in ApJ, also available with full resolution figures at http://www.strw.leidenuniv.nl/~klessen/Preprint

Genetic Burden for Late-Life Neurodegenerative Disease and Its Association With Early-Life Lipids, Brain, Behavior, and Cognition

Background: Genetics play a significant role in the etiology of late-life neurodegenerative diseases like Alzheimer’s disease, Parkinson’s disease, and frontotemporal dementia. Part of the individual differences in risk for these diseases can be traced back decades before the onset of disease symptoms. Previous studies have shown evidence for plausible links of apolipoprotein E (APOE), the most important genetic marker for Alzheimer’s disease, with early-life cognition and neuroimaging markers. We aimed to assess whether genome-wide genetic burden for the aforementioned neurodegenerative diseases plays a role in early-life processes. Methods: We studied children from the Generation R Study, a prospective birth cohort. APOE genotypes and polygenic genetic burdens for Alzheimer’s disease, Parkinson’s disease, and frontotemporal dementia were obtained through genome-wide genotyping. Non-verbal intelligence was assessed through cognitive tests at the research center around the age of 6 years, and educational attainment through a national school performance test around the age of 11 years. The Child Behavior Checklist was administered around the age of 10 years, and data from the anxious/depressed, withdrawn/depressed, and the internalizing behavior problems scales were used. Children participated in a neuroimaging study when they were 10 years old, in which structural brain metrics were obtained. Lipid serum profiles, which may be influenced by APOE genotype, were assessed from venal blood obtained around the age of 6 years. The sample size per analysis varied between 1,641 and 3,650 children due to completeness of data. Results: We did not find evidence that APOE genotype or the polygenic scores impact on childhood nonverbal intelligence, educational attainment, internalizing behavior, and global brain structural measures including total brain volume and whole brain fractional anisotropy (all p > 0.05). Carriership of the APOE ε2 allele was associated with lower and APOE ε4 with higher low-density lipoprotein cholesterol concentrations when compared to APOE ε3/ε3 carriers. Conclusion: We found no evidence that genetic burden for late-life neurodegenerative diseases associates with early-life cognition, internalizing behavior, or global brain structure

Genetic scores for adult subcortical volumes associate with subcortical volumes during infancy and childhood

Individual differences in subcortical brain volumes are highly heritable. Previous studies have identified genetic variants that underlie variation in subcortical volumes in adults. We tested whether those previously identified variants also affect subcortical regions during infancy and early childhood. The study was performed within the Generation R study, a prospective birth cohort. We calculated polygenic scores based on reported GWAS for volumes of the accumbens, amygdala, brainstem, caudate nucleus, globus pallidus, putamen, and thalamus. Participants underwent cranial ultrasound around 7 weeks of age (range: 3–20), and we obtained metrics for the gangliothalamic ovoid, a predecessor of the basal ganglia. Furthermore, the children participated in a magnetic resonance imaging (MRI) study around the age of 10 years (range: 9–12). A total of 340 children had complete data at both examinations. Polygenic scores primarily associated with their corresponding volumes at 10 years of age. The scores also moderately related to the diameter of the gangliothalamic ovoid on cranial ultrasound. Mediation analysis showed that the genetic influence on subcortical volumes at 10 years was only mediated for 16.5–17.6% of the total effect through the gangliothalamic ovoid diameter at 7 weeks of age. Combined, these findings suggest that previously identified genetic variants in adults are relevant for subcortical volumes during early life, and that they affect both prenatal and postnatal development of the subcortical regions

The Risk of Dementia in Relation to Cognitive and Brain Reserve

Background: Individual differences in the risk to develop dementia remain poorly understood. These differences may partly be explained through reserve, which is the ability to buffer cognitive decline due to neuropathology and age. Objective: To determine how much early and late–life cognitive reserve (CR) and brain reserve (BR) contribute to the risk of dementia. Methods: 4,112 dementia-free participants (mean age = 66.3 years) from the Rotterdam Study were followed up for on average 6.0 years. Early-life CR and BR were defined as attained education and intracranial volume, respectively. Late-life CR was derived through variance decomposition based on cognition. Late-life BR was set as the total non-lesioned brain volume divided by intracranial volume. Results: Higher early-life CR (hazard ratio = 0.48, 95% CI = [0.21; 1.06]) but not early-life BR associated with a lower risk of incident dementia. Higher late-life CR (hazard ratio = 0.57, 95% CI = [0.48; 0.68]) and late-life BR (hazard ratio = 0.54, 95% CI = [0.43; 0.68]) also showed lower levels of dementia. Combining all proxies into one model attenuated the association between early-life CR and dementia (hazard ratio = 0.56, 95% CI = [0.25; 1.25]) whereas the other associations were unaffected. These findings were stable upon stratification for sex, age, and APOE ɛ4. Finally, high levels of l

White matter microstructure correlates of age, sex, handedness and motor ability in a population-based sample of 3031 school-age children

Understanding the development of white matter microstructure in the general population is an imperative precursor to identifying its involvement in psychopathology. Previous studies have reported changes in white matter microstructure associated with age and different developmental patterns between boys and girls. Handedness has also been related to white matter in adults. Motor performance, tightly dependent on overall neuronal myelination, has been related to the corpus callosum. However, the association between motor performance and global white matter microstructure has not been reported in the literature. In general, these age, sex, handedness, and motor performance associations have been observed using small and poorly representative samples. We examined the rela

Design and overview of the Origins of Alzheimer’s Disease Across the Life course (ORACLE) study

Brain development and deterioration across the lifespan are integral to the etiology of late-life neurodegenerative disease. Factors that influence the health of the adult brain remain to be elucidated and include risk factors, protective factors, and factors related to cognitive and brain reserve. To address this knowledge gap we designed a life-course study on brain health, which received funding through the EU ERC Programme under the name Origins of Alzheimer’s Disease Across the Life course (ORACLE) Study. The ORACLE Study is embedded within Generation R, a prospective population-based cohort study of children and their parents, and links this with the Rotterdam Study, a population-based study in middle-aged and elderly persons. The studies are based in Rotterdam, the Netherlands. Generation R focuses on child health from fetal life until adolescence with repeated in-person examinations, but has also included data collection on the children’s parents. The ORACLE Study aims to extend the parental data collection in nearly 2000 parents with extensive measures on brain health, including neuroimaging, cognitive testing and motor testing. Additionally, questionnaires on migraine, depressive symptoms, sleep, and neurological family history were completed. These data allow for the investigation of longitudinal influences on adult brain health as well as intergenerational designs involving children and parents. As a secondary focus, the sampling is enriched by mothers (n = 356) that suffered from hypertensive disorders during pregnancy in order to study brain health in this high-risk population. This article provides an overview of the rationale and the design of the ORACLE Study