High-resolution Computer Simulations Research Articles

Variance effective population size is affected by census size in sub-structured populations.

Measurement of allele frequency shifts between temporally spaced samples has long been used for assessment of effective population size (Ne ), and this 'temporal method' provides estimates of Ne referred to as variance effective size (NeV ). We show that NeV of a local population that belongs to a sub-structured population (a metapopulation) is determined not only by genetic drift and migration rate (m), but also by the census size (Nc ). The realized NeV of a local population can either increase or decrease with increasing m, depending on the relationship between Ne and Nc in isolation. This is shown by explicit mathematical expressions for the factors affecting NeV derived for an island model of migration. We verify analytical results using high-resolution computer simulations, and show that the phenomenon is not restricted to the island model migration pattern. The effect of Nc on the realized NeV of a local subpopulation is most pronounced at high migration rates. We show that Nc only affects local NeV , whereas NeV for the metapopulation as a whole, inbreeding (NeI ), and linkage disequilibrium (NeLD ) effective size are all independent of Nc . Our results provide a possible explanation to the large variation of Ne /Nc ratios reported in the literature, where Ne is frequently estimated by NeV . They are also important for the interpretation of empirical Ne estimates in genetic management where local NeV is often used as a substitute for inbreeding effective size, and we suggest an increased focus on metapopulation NeV as a proxy for NeI .

An S-Shaped Aβ42 Cross-β Hexamer Embedded into a Lipid Bilayer Reveals Membrane Disruption and Permeability.

The interactions of amyloid oligomers with membranes are known to contribute to cellular toxicity. Numerous in vitro experimental studies reported on the insertion of oligomers of different sizes that can induce cell membrane disruption, extract lipids, and form ion-permeable transmembrane pores. The current repertoire of amyloid-beta (Aβ) membrane-inserted folds that was subject to high-resolution structure NMR spectroscopy and computer simulations is devoid of any cross-β fibrillar structure. In this study, we explored the dynamics of an S-shaped Aβ42 cross-β hexamer model inserted into a lipid bilayer membrane by two atomistic molecular dynamics simulations. The initial model is characterized by the hydrophobic residues at the central hydrophobic core (residues 17-21, CHC) and the C-terminus (residues 30-42) embedded into the membrane. We observed major structural secondary, tertiary, and quaternary rearrangements leading to two distinct species, hexamer and two trimers, accompanied by membrane disruption and water permeation. The simulations show that some configurations, but not the majority, have the CHC and C-terminus hydrophobic residues exposed to the solvent. Overall, our computational results offer new perspectives to understand the relationship between Aβ42 assemblies and membrane permeability.

Advances in machine learning applications for cardiovascular 4D flow MRI.

Four-dimensional flow magnetic resonance imaging (MRI) has evolved as a non-invasive imaging technique to visualize and quantify blood flow in the heart and vessels. Hemodynamic parameters derived from 4D flow MRI, such as net flow and peak velocities, but also kinetic energy, turbulent kinetic energy, viscous energy loss, and wall shear stress have shown to be of diagnostic relevance for cardiovascular diseases. 4D flow MRI, however, has several limitations. Its long acquisition times and its limited spatio-temporal resolutions lead to inaccuracies in velocity measurements in small and low-flow vessels and near the vessel wall. Additionally, 4D flow MRI requires long post-processing times, since inaccuracies due to the measurement process need to be corrected for and parameter quantification requires 2D and 3D contour drawing. Several machine learning (ML) techniques have been proposed to overcome these limitations. Existing scan acceleration methods have been extended using ML for image reconstruction and ML based super-resolution methods have been used to assimilate high-resolution computational fluid dynamic simulations and 4D flow MRI, which leads to more realistic velocity results. ML efforts have also focused on the automation of other post-processing steps, by learning phase corrections and anti-aliasing. To automate contour drawing and 3D segmentation, networks such as the U-Net have been widely applied. This review summarizes the latest ML advances in 4D flow MRI with a focus on technical aspects and applications. It is divided into the current status of fast and accurate 4D flow MRI data generation, ML based post-processing tools for phase correction and vessel delineation and the statistical evaluation of blood flow.

How nanoporous silicon-polypyrrole hybrids flex their muscles in aqueous electrolytes: In operando high-resolution x-ray diffraction and electron tomography-based micromechanical computer simulations

Macroscopic strain experiments revealed that Si crystals traversed by parallel, channel-like nanopores functionalized with the muscle polymer polypyrrole exhibit large and reversible electrochemo-mechanical actuation in aqueous electrolytes. On the microscopical level this system still bears open questions, as to how the electrochemical expansion and contraction of PPy acts on to np-Si pore walls and how the collective motorics of the pore array emerges from the single-nanopore behavior. An analysis of in operando X-ray diffraction experiments with micromechanical finite element simulations, based on a 3D reconstruction of the nanoporous medium by TEM tomography, shows that the in-plane mechanical response is dominantly isotropic despite the anisotropic elasticity of the single crystalline host matrix. However, the structural anisotropy originating from the parallel alignment of the nanopores lead to significant differences between the in- and out-of-plane electromechanical response. This response is not describable by a simple 2D arrangement of parallel cylindrical channels. Rather, the simulations highlight that the dendritic shape of the Si pore walls, including pore connections between the main channels, cause complex, inhomogeneous stress-strain fields in the crystalline host. Time-dependent X-ray scattering on the dynamics of the actuator properties hint towards the importance of diffusion limitations, plastic deformation and creep in the nanoconfined polymer upon (counter-)ion adsorption and desorption, the very pore-scale processes causing the macroscopic electroactuation. From a more general perspective, our study demonstrates that the combination of TEM tomography-based micromechanical modeling with high-resolution X-ray scattering experiments provides a powerful approach for in operando analysis of nanoporous composites from the single-nanopore up to the porous-medium scale.

Characteristics of Earthquake Cycles: A Cross-Dimensional Comparison of 0D to 3D Numerical Models.

High‐resolution computer simulations of earthquake sequences in three or even two dimensions pose great demands on time and energy, making lower‐cost simplifications a competitive alternative. We systematically study the advantages and limitations of simplifications that eliminate spatial dimensions in quasi‐dynamic earthquake sequence models, from 3D models with a 2D fault plane down to 0D or 1D models with a 0D fault point. We demonstrate that, when 2D or 3D models produce quasi‐periodic characteristic earthquakes, their behavior is qualitatively similar to lower‐dimension models. Certain coseismic characteristics like stress drop and fracture energy are largely controlled by frictional parameters and are thus largely comparable. However, other observations are quantitatively clearly affected by dimension reduction. We find corresponding increases in recurrence interval, coseismic slip, peak slip velocity, and rupture speed. These changes are to a large extent explained by the elimination of velocity‐strengthening patches that transmit tectonic loading onto the velocity‐weakening fault patch, thereby reducing the interseismic stress rate and enhancing the slip deficit. This explanation is supported by a concise theoretical framework, which explains some of these findings quantitatively and effectively estimates recurrence interval and slip. Through accounting for an equivalent stressing rate at the nucleation size h* into 2D and 3D models, 0D or 1D models can also effectively simulate these earthquake cycle parameters. Given the computational efficiency of lower‐dimensional models that run more than a million times faster, this paper aims to provide qualitative and quantitative guidance on economical model design and interpretation of modeling studies.

Conceptual Design of a Hybrid Hydrogen Fuel Cell/Battery Blended-Wing-Body Unmanned Aerial Vehicle—An Overview

The manuscript presents the conceptual design phase of an unmanned aerial vehicle, with the objective of a systems approach towards the integration of a hydrogen fuel-cell system and Li-ion batteries into an aerodynamically efficient platform representative of future aircraft configurations. Using a classical approach to aircraft design and a combination of low- and high-resolution computational simulations, a final blended wing body UAV was designed with a maximum take-off weight of 25 kg and 4 m wingspan. Preliminary aerodynamic and propulsion sizing demonstrated that the aircraft is capable of completing a 2 h long mission powered by a 650 W fuel cell, hybridized with a 100 Wh battery pack, and with a fuel quantity of 80 g of compressed hydrogen.

Atmospheric pollution from rockets

We address the impact of rocket exhaust gases on atmospheric pollution through high-resolution computational fluid dynamics simulations. We have modeled the exhaust gases and developing plume at several altitudes along a typical trajectory of a standard present-day rocket, as a prototypical example of a two-stage rocket to transport people and payloads into Earth's orbit and beyond. The modeled rocket uses RP-1 as the propellant and liquid oxygen as the oxidizer to generate ∼6806 kN of thrust via a total of nine nozzles, matching—as closely as possible based on available data—the specifications to the Thaicom 8 launch mission of the Falcon 9 rocket manufactured by SpaceX. We have used high-order discretization methods, 11th-order accurate, in conjunction with implicit large eddy simulations to model exhaust gas mixing, dispersion, and heat transfer into the atmosphere at altitudes up to 67 km. We show that pollution from rockets should not be underestimated as frequent future rocket launches could have a significant cumulative effect on climate. The production of thermal nitrogen oxides can remain considerable up to altitudes with an ambient atmospheric pressure below but of the same order of magnitude as the nozzles exit pressure. At the same time, the emitted mass of carbon dioxide in the mesosphere is equivalent to that contained in 26 km3 of atmospheric air at the same altitude.

Core-Satellite Gold Nanoparticle Complexes Grown by Inert Gas-Phase Condensation.

Spontaneous growth of complexes consisted of a number of individual nanoparticles in a controlled manner, particularly in demanding environments of gas-phase synthesis, is a fascinating opportunity for numerous potential applications. Here, we report the formation of such core–satellite gold nanoparticle structures grown by magnetron sputtering inert gas condensation. Combining high-resolution scanning transmission electron microscopy and computational simulations, we reveal the adhesive and screening role of H2O molecules in formation of stable complexes consisted of one nanoparticle surrounded by smaller satellites. A single layer of H2O molecules, condensed between large and small gold nanoparticles, stabilizes positioning of nanoparticles with respect to one another during milliseconds of the synthesis time. The lack of isolated small gold nanoparticles on the substrate is explained by Brownian motion that is significantly broader for small-size particles. It is inferred that H2O as an admixture in the inert gas condensation opens up possibilities of controlling the final configuration of the different noble metal nanoparticles.

Numerical investigation of quasi-sessile droplet absorption into wound dressing capillaries

The key concept in wound dressing design and development is the fact that keeping a wound moist accelerates healing. Therefore, the selection of the appropriate wound dressing type is vital. The absorption of wound exudate by wound dressings can be considered as a microfluidic phenomenon that can be investigated either by performing high resolution laboratory experiments or by utilizing high resolution Computational Fluid Dynamics numerical simulations. As an initial step, in the present paper, the effects of the pore size (wound dressing porosity), the liquid (wound exudate) viscosity, and the initial droplet diameter are numerically investigated using a simplified analog of the phenomenon that consists of a quasi-sessile droplet being absorbed by a single cylindrical pore. For this purpose, an enhanced Volume Of Fluid model, developed in the general context of OpenFOAM, is validated and applied. It is found that distinct droplet absorption rates exist with specific relationships derived using best-fit lines that can predict the absorption rates for particular values of pore size and liquid viscosity. For the examined Eo and Oh number ranges (0.0015 < Eo < 0.15 and 0.0035 < Oh < 0.095), these distinct droplet absorption rates are directly linked with four different droplet evolution regimes that are grouped in a well-defined flow map. Finally, it is shown that the resulting liquid absorption rates are not significantly affected by the initial droplet diameter and that an appropriate wound dressing porosity can be selected by an estimation of the wound exudate physical properties.

Reducing aerosol dispersion by high flow therapy in COVID-19: High resolution computational fluid dynamics simulations of particle behavior during high velocity nasal insufflation with a simple surgical mask.

ObjectiveAll respiratory care represents some risk of becoming an aerosol‐generating procedure (AGP) during COVID‐19 patient management. Personal protective equipment (PPE) and environmental control/engineering is advised. High velocity nasal insufflation (HVNI) and high flow nasal cannula (HFNC) deliver high flow oxygen (HFO) therapy, established as a competent means of supporting oxygenation for acute respiratory distress patients, including that precipitated by COVID‐19. Although unlikely to present a disproportionate particle dispersal risk, AGP from HFO continues to be a concern. Previously, we published a preliminary model. Here, we present a subsequent highresolution simulation (higher complexity/reliability) to provide a more accurate and precise particle characterization on the effect of surgical masks on patients during HVNI, low‐flow oxygen therapy (LFO2), and tidal breathing.MethodsThis in silico modeling study of HVNI, LFO2, and tidal breathing presents ANSYS fluent computational fluid dynamics simulations that evaluate the effect of Type I surgical mask use over patient face on particle/droplet behavior.ResultsThis in silico modeling simulation study of HVNI (40 L min−1) with a simulated surgical mask suggests 88.8% capture of exhaled particulate mass in the mask, compared to 77.4% in LFO2 (6 L min−1) capture, with particle distribution escaping to the room (> 1 m from face) lower for HVNI+Mask versus LFO2+Mask (8.23% vs 17.2%). The overwhelming proportion of particulate escape was associated with mask‐fit designed model gaps. Particle dispersion was associated with lower velocity.ConclusionsThese simulations suggest employing a surgical mask over the HVNI interface may be useful in reduction of particulate mass distribution associated with AGPs.

Morphological and Hemodynamic Factors Associated with Ruptured Middle Cerebral Artery Mirror Aneurysms: A Retrospective Study

Mirror intracranial aneurysms with different rupture status is a useful model to investigate features associated with aneurysm rupture. Morphological and hemodynamic analyses of ruptured middle cerebral artery (MCA) mirror aneurysms are rarely reported. The purpose of this study was to determine the morphological or hemodynamic characteristics associated with ruptured MCA mirror aneurysms. We performed a retrospective analysis of consecutive 317 patients with MCA aneurysms. Ruptured MCA mirror aneurysms (1 ruptured and mirror unruptured aneurysm) were included. In the matched pairs of ruptured and unruptured mirror aneurysms, 13 morphological parameters were measured using 3-dimensional computed tomography angiography and 6 hemodynamic parameters were evaluated using high-resolution computational fluid dynamic simulations. The association of morphological and hemodynamic characteristics with the rupture of MCA mirror aneurysms was determined. A total of 20 (6.31%) patients with 40 MCA mirror aneurysms were included in this study. There were significant differences in morphological and hemodynamic parameters between the ruptured and unruptured mirror aneurysms. Irregular aneurysms were 3 times more common in the ruptured aneurysms than in the unruptured aneurysms. A larger aneurysm (P= 0.025), a higher aneurysm (P= 0.020), a larger size ratio (P= 0.009), a higher bottleneck ratio (P= 0.033), an irregular aneurysm (P= 0.022), a higher maximum intra-aneurysmal wall shear stress (WSS; P= 0.020), and a lower normalized average WSS (P= 0.008) were associated with MCA mirror aneurysm rupture. Larger aneurysms, a larger size ratio, irregular aneurysms, a lower spatial average WSS, and a higher maximum WSS may contribute to evaluating the risk of rupture of MCA aneurysms independent of patient characteristics.

Computational characterization of the secondary droplets formed during the impingement of a train of ethanol drops

This article uniquely characterizes the secondary droplets formed during the impingement of a train of ethanol drops, using three-dimensional direct numerical simulations performed under conditions studied experimentally by Yarin and Weiss. Our numerical results have been previously validated against experimental data demonstrating the ability to accurately capture the splashing dynamics. In this work, the predictive ability of the model is leveraged to gain further insight into secondary droplet formation. We present a robust post-processing algorithm, which scrutinizes the liquid volume fraction field in the volume-of-fluid method and quantifies the number, volume and velocity of secondary droplets. The high-resolution computational simulations enable secondary droplet characterization within close proximity of the impingement point at small length and time scales, which is extremely challenging to achieve experimentally. By studying the temporal evolution of secondary droplet formation, direct connections are made between liquid structures seen in the simulation and the instantaneous distribution of secondary droplets, leading to detailed insight into the instability-driven breakup process of lamellae. Time-averaged secondary droplet characteristics are also studied to describe the global distribution of secondary droplets. Such analysis is vital to understanding fuel drop impingement in direct injection engines, facilitating the development of highly accurate spray–wall interaction models for use in Lagrangian solvers.

Ambient air quality and human health in India

TPS 682: Long-term health effects of air pollutants 2, Exhibition Hall, Ground floor, August 27, 2019, 3:00 PM - 4:30 PM Background: India experiences levels of ambient fine particles (PM2.5) and ozone (O3) amongst the highest globally, where exposure is a leading risk factor for human health. Air pollutant emissions are predicted to increase in India. However, Indian air quality remains understudied and knowledge of the sources causing air pollution is limited. Methods: We quantify the contribution of different sources to the disease burden from ambient air pollution exposure in India and the effects of future air pollution control pathways. We combined high-resolution computer simulations, new observations, and updated exposure-response relationships. Results: Ambient PM2.5 exposure causes 1 million premature deaths each year in India, where large reductions in emissions will be required to reduce the health burden due to the non-linear exposure-response relationship causing health effects to saturate at high exposures. The disease burden from ambient O3 exposure is 200% larger than previously thought, causing 124,000 premature deaths every year. Residential energy use emissions dominate ambient PM2.5 concentrations (52%) and are attributed to 511,000 premature deaths. However, removing these emissions would avert only 256,000 premature deaths due to the non-linear exposure-response relationship. Emissions from land transport dominate the ambient O3 disease burden (35%), followed by power generation (23%). Under current policies to 2050, annual premature mortality from PM2.5 and O3 exposure will increase by 68% and 204%, respectively, due to population ageing and growth increasing susceptibility. Stringent air pollution control pathways can offset the increase in premature mortality from population ageing and growth by 91% (610,000 deaths) for PM2.5 and 45% (335,000 deaths) for O3, and reduce the overall mortality rate from ambient PM2.5 exposure by 15%. Conclusions: The disease burden from air pollution exposure in India is substantial and likely to increase unless stringent air pollution management provide large emission reductions. A focus should be to reduce solid fuel combustion.

Flame evolution in shock-accelerated flow under different reactive gas mixture gradients.

The interaction between a planar shock wave and a spherical flame is studied numerically for an ethylene-oxygen-nitrogen gas mixture. Influences of different initial reactive gas mixture gradients on the shock-flame interaction are investigated by using high-resolution computational simulations. The results show that the different reactive gas mixture gradients can greatly affect the flame evolution in shock accelerated flow. A detonation only emerges in the homogenous reactive gas mixture case, but a distinct shock bifurcation can be found in the inhomogeneous cases where the leftward reflected shock wave propagates in a reverse flow with a high transverse velocity gradient in the inhomogeneous cases. Also, the flame volume and heat release rate increase when the distribution of the reactive gas mixture is uniform or with a positive gradient in this paper, but decrease when the distribution of the reactive gas mixture is with a negative gradient, however, the ratio of unburned to burned regions in the flame zone shows just the opposite trends. Furthermore, the factors affecting the vorticity generation are also analyzed. It is found that the compression term has a relatively stronger influence on the vorticity generation in all the three cases except the period before the reflected shock wave impinges on the distorted flame in the homogeneous case, wherein the baroclinic effect dominates the vorticity generation in the flame zone.

Numerical investigation of planar shock wave impinging on spherical gas bubble with different densities

The interaction between a planar shock wave and a spherical gas bubble containing sulfur hexafluoride, Refrigerant-22, neon, or helium is studied numerically. Influences of the Atwood number (At) on the evolution of the shock wave and gas bubble are clarified by using high-resolution computational simulations. The results show that the difference in the physical properties between the ambient air and the gas bubble has a significant influence on the evolution of wave pattern and bubble deformation. For the fast/slow configuration (At > 0) in the present study (At = 0.67 and 0.51), the incident shock focuses near the interior right interface to form an outward jet. Besides, the mixedness, average vorticity, and the absolute value of circulation all increase as the Atwood number increases. By contrast, for the slow/fast configuration (At < 0) with At = −0.19 and −0.76, the rotational directions of the vorticities formed at the same position are reversed compared with those in the fast/slow configuration, which induces an inward air jet to impact on the gas bubble from the outside. In addition, the mixedness, average vorticity, and the absolute value of circulation all increase as the Atwood number decreases. Nevertheless, regardless of At > 0 or At < 0, the effective volume of the gas bubble basically decreases when the Atwood number decreases. Hence, on the whole, the Atwood number has a nonmonotonic influence on the evolution of effective volume of gas bubble, mixedness, average vorticity, and circulation simultaneously.

Formation mechanism of twin structures in p-type (Bi0.25Sb0.75)2Te3 thermoelectric compound

The formation mechanism of twin structures in p-type (Bi0.25Sb0.75)2Te3 compound was examined using high-resolution transmission electron microscopy (HR-TEM) and computer simulations. The results shown that the formation of twins is analogous to the twinning mechanism via synchronized activation of Shockley partial dislocations commonly observed terminating {111} growth and annealing twins in face centered cubic (FCC) metals. The 101¯0 boundary, as an incoherent twin boundary (ITB), is mobile due to its lower shear stress compared to that of the coherent {0001} twin boundary; thickness of the twin region can be reduced or increased according to the direction of the movement.

High-resolution dynamic computer simulation of electrophoresis using a multiphysics software platform

The modeling and simulation software COMSOL Multiphysics® was recently extended with an electrophoretic transport interface. Its performance was investigated by comparison to results obtained using the 1D dynamic electrophoresis simulators GENTRANS and SIMUL5. Simulations of zone electrophoresis, isotachophoresis, isoelectric focusing and of an oscillating electrolyte system were performed. Smooth profiles were essentially identical indicating that the COMSOL electrophoretic transport interface is able to reproduce results of the 1D simulators. Differences in the way the respective numerical schemes handle steep concentration gradients and associated instabilities were observed. The COMSOL electrophoretic transport interface is expected to be useful as a general model for simulations in 1D, 2D or 3D geometries, as well as for simulations combining electrophoresis with other physical phenomena.

Raziskave oborin v aluminijevih zlitinah z visokoresolucijsko elektronsko mikroskopijo in računalniško simulacijo

Raziskave oborin v aluminijevih zlitinah z visokoresolucijsko elektronsko mikroskopijo in računalniško simulacijo

The case of the missing satellites

In the late 1990s, computational technology had advanced sufficiently that astrophysicists were able to construct reasonably high resolution computer simulations of the Local Group of galaxies. These simulations indicated there should be around 250 small satellite galaxies orbiting the Milky Way and Andromeda. In the real Local Group, however, only around 40 satellites had been observed, and only twenty or so more have been discovered since then. Despite this discrepancy in numbers, claims have been made in recent years that the ‘missing satellites problem’ has been solved. Using the examples of the constructed luminosity curve, and hydrodynamic simulations, this paper explores how simulations are used in conjunction with observation to ‘solve’ the missing satellites problem. It is suggested that the simulated universes have sufficient complexity to be (temporarily) understood as worlds in their own right, ones that can be measured and observed. By demonstrating that these virtual worlds are sufficiently ‘realistic’ with respect to observations, astrophysicists are able to make a robust argument for the existence of ‘dark’, non-observable astrophysical objects. Observational and simulated data are combined to demonstrate the plausibility—a term that develops more ontologically meaningful connotations—of both the existence and the maintenance of dark satellites. It is thus through the conflation of the real and virtual worlds, the blending of simulation data with empirical data, that the missing satellites problem is ‘solved’.

Introducing SiTTE: A controlled laboratory setting to study the impact of turbulent fluctuations on light propagation in the underwater environment.

Small-scale spatial variation in temperature can lead to localized changes in the index of refraction and can distort electro-optical (EO) signal transmission in ocean and atmosphere. This phenomenon is well-studied in the atmosphere, where it is generally called "optical turbulence". Less is known about how turbulent fluctuations in the ocean distort EO signal transmissions, an effect that can impact various underwater applications, from diver visibility to active and passive remote sensing. To provide a test bed for the study of the impacts from turbulent flows on EO signal transmission, and to examine and mitigate turbulence effects, we set up a laboratory turbulence environment allowing the controlled and repeatable variation of turbulence intensity. The laboratory measurements are complemented by high resolution computational fluid dynamics simulations emulating the tank environment. This controlled Simulated Turbulence and Turbidity Environment (SiTTE) can be used to assess optical image degradation in the tank in relation to turbulence intensity, as well as to examine various adaptive optics mitigation techniques.