In situ visualization of large-scale turbulence simulations in Nek5000 with ParaView Catalyst

In situ visualization on high-performance computing systems allows us to analyze simulation results that would otherwise be impossible, given the size of the simulation data sets and offline post-processing execution time. We develop an in situ adaptor for Paraview Catalyst and Nek5000, a massively parallel Fortran and C code for computational fluid dynamics. We perform a strong scalability test up to 2048 cores on KTH’s Beskow Cray XC40 supercomputer and assess in situ visualization’s impact on the Nek5000 performance. In our study case, a high-fidelity simulation of turbulent flow, we observe that in situ operations significantly limit the strong scalability of the code, reducing the relative parallel efficiency to only ≈ 21 % on 2048 cores (the relative efficiency of Nek5000 without in situ operations is ≈ 99 %). Through profiling with Arm MAP, we identified a bottleneck in the image composition step (that uses the Radix-kr algorithm) where a majority of the time is spent on MPI communication. We also identified an imbalance of in situ processing time between rank 0 and all other ranks. In our case, better scaling and load-balancing in the parallel image composition would considerably improve the performance of Nek5000 with in situ capabilities. In general, the result of this study highlights the technical challenges posed by the integration of high-performance simulation codes and data-analysis libraries and their practical use in complex cases, even when efficient algorithms already exist for a certain application scenario

13C-assisted metabolic flux analysis to investigate heterotrophic and mixotrophic metabolism in Cupriavidus necator H16

Introduction. Cupriavidus necator H16 is a gram-negative bacterium, capable of lithoautotrophic growth by utilizing hydrogen as an energy source and fixing carbon dioxide (CO2) through Calvin-Benson-Bassham (CBB) cycle. The potential to utilize synthesis gas (Syngas) and the prospects of rerouting carbon from polyhydroxybutyrate synthesis to value-added compounds makes C. necator an excellent chassis for industrial application. Objectives. In the context of lack of sufficient quantitative information of the metabolic pathways and to advance in rational metabolic engineering for optimized product synthesis in C. necator H16, we carried out a metabolic flux analysis based on steady-state 13C-labelling. Methods. In this study, steady-state carbon labelling experiments, using either D-[1-13C]fructose or [1,2-13C]glycerol, were undertaken to investigate the carbon flux through the central carbon metabolism in C. necator H16 under heterotrophic and mixotrophic growth conditions, respectively. Results. We found that the CBB cycle is active even under heterotrophic condition, and growth is indeed mixotrophic. While Entner-Doudoroff (ED) pathway is shown to be the major route for sugar degradation, tricarboxylic acid (TCA) cycle is highly active in mixotrophic condition. Enhanced flux is observed in reductive pentose phosphate pathway (redPPP) under the mixotrophic condition to supplement the precursor requirement for CBB cycle. The flux distribution was compared to the mRNA abundance of genes encoding enzymes involved in key enzymatic reactions of the central carbon metabolism. Conclusion. This study leads the way to establishing 13C-based quantitative fluxomics for rational pathway engineering in C. necator H16

Electromagnetic Characteristics of the Soil

The electromagnetic characteristics of the soil are discussed in this chapter. The characteristics of porous bedrock, soil medium, and impacts of rain attenuations are also presented. The models of dielectric soil properties are studied with a rigorous focus on the constitutive parameters of subsurface soil medium. Moreover, the permittivity and wavenumber in soil are explained. In addition, the frequency-dependent dielectric properties such as dispersion in soil, absorption characteristic, and penetration depth versus frequency are reviewed. Furthermore, the effective permittivity of soil–water mixture for through-the soil-propagation mechanism is analyzed thoroughly

Wireless Underground Channel Modeling

A comprehensive treatment of wireless underground channel modeling is presented in this chapter. The impacts of the soil on bandwidth and path loss are analyzed. A mechanism for the UG channel sounding and multipath characteristics analysis is discussed. Moreover, novel time-domain impulse response model for WUC is reviewed with the explanation of model parameters and statistics. Furthermore, different types of the through-the-soil wireless communications are surveyed. Finally, the chapter concludes with discussion of the UG wireless statistical model and path loss model for through-the-soil wireless communications in decision agriculture. The model presented in this chapter is also validated with empirical data

Signals in the Soil: Underground Antennas

Antenna is a major design component of Internet of Underground Things (IOUT) communication system. The use of antenna, in IOUT, differs from traditional communication in that it is buried in the soil. Therefore, one of the main challenges, in IOUT applications, is to establish a reliable communication. To that end, there is a need of designing an underground-specific antenna. Three major factors that can impact the performance of a buried antenna are: (1) effect of high soil permittivity changes the wavelength of EM waves, (2) variations in soil moisture with time affecting the permittivity of the soil, and (3) difference in how EM waves propagate during aboveground (AG) and underground (UG) communications. For the third challenge above, it is to be noted that lateral waves are dominant component in EM during UG2UG communication and suffer lowest attenuation as compared to other, direct and reflected, components. Therefore, antennas used for over-the-air (OTA) communication will not be suitable for UG communication because of impedance mismatch. This chapter focuses on developing a theoretical model for understanding the impact of soil on antenna by conducting experiments in different soil types (silty clay loam, sandy, and silt loam soil) and indoor testbed. The purpose of the model is to predict UG antenna resonance for designing efficient communication system for IOUT. Based on the model a wideband planar antenna is designed considering soil dispersion and soil–air interface reflection effect which improves the communication range five times from the antennas designed only for the wavelength change in soil. Furthermore, it also focuses on developing an impedance model to study the effect of changing wavelength in underground communication. It is also discussed how soil–air interface and soil properties effect the return loss of dipole antenna

Internet of Things in Water Management and Treatment

The goal of the water security IoT chapter is to present a comprehensive and integrated IoT based approach to environmental quality and monitoring by generating new knowledge and innovative approaches that focus on sustainable resource management. Mainly, this chapter focuses on IoT applications in wastewater and stormwater, and the human and environmental consequences of water contaminants and their treatment. The IoT applications using sensors for sewer and stormwater monitoring across networked landscapes, water quality assessment, treatment, and sustainable management are introduced. The studies of rate limitations in biophysical and geochemical processes that support the ecosystem services related to water quality are presented. The applications of IoT solutions based on these discoveries are also discussed

Internet of Things for Sustainable Forestry

Forests and grasslands play an important role in water and air purification, prevention of the soil erosion, and in provision of habitat to wildlife. Internet of Things has a tremendous potential to play a vital role in the forest ecosystem management and stability. The conservation of species and habitats, timber production, prevention of forest soil degradation, forest fire prediction, mitigation, and control can be attained through forest management using Internet of Things. The use and adoption of IoT in forest ecosystem management is challenging due to many factors. Vast geographical areas and limited resources in terms of budget and equipment are some of the limiting factors. In digital forestry, IoT deployment offers effective operations, control, and forecasts for soil erosion, fires, and undesirable depositions. In this chapter, IoT sensing and communication applications are presented for digital forestry systems. Different IoT systems for digital forest monitoring applications are also discussed

Signals in the Soil: An Introduction to Wireless Underground Communications

In this chapter, wireless underground (UG) communications are introduced. A detailed overview of WUC is given. A comprehensive review of research challenges in WUC is presented. The evolution of underground wireless is also discussed. Moreover, different component of UG communications is wireless. The WUC system architecture is explained with a detailed discussion of the anatomy of an underground mote. The examples of UG wireless communication systems are explored. Furthermore, the differences of UG wireless and over-the-air wireless are debated. Different types of wireless underground channel (e.g., In-Soil, Soil-to-Air, and Air-to-Soil) are reported as well

SUGAR BEET RESPONSE TO BALANCED NITROGEN FERTILIZATION WITH PHOSPHORUS AND POTASSIUM PART I. DYNAMICS OF BEET YIELD DEVELOPMENT

Abstract BARLOG, P., W. GRZEBISZ, K. PEPLINSKI and W. SZCZEPANIAK, 2013. Sugar beet response to balanced nitrogen fertilization with phosphorus and potassium. Part I. Dynamics of beet yield development. Bulg. J. Agric. Sci., 19: 1311-1318 The objective of the conducted study was to determine the effect of various levels of P, K under the background of constant N rate on dynamics of sugar beet root yield. The field trial, arranged as a factorial design, was consisted of eight treatments: N 0 P 0 K 0 ; N 0 P 1 K 1 ; N 1 P 0 K 1 ; N 1 P 1 K 0 ; N 1 P 0.25 K 0.25 ; N 1 P 0.5 K 1 ; N 1 P 1 K 1 and N 1 P 1 K 1 +Ca; where 1 is recommended level of N, P, K application and Ca means that phosphorus applied as partially acidulated phosphoric rock (PAPR). The in-season yield sampling was conducted at 92, 113, 134, 155 and 175 th day after sowing. The highest degree of yield potential realization revealed in the year with favourable weather conditions. The highest yield was harvested on the plot fertilized with N 1 P 1 K 1 +Ca. In years with extended drought, sugar beet achieved the maximum yield in the treatment N 1 P 0.25 K 0.25 . Phosphorus revealed as the key yield forming factors, i.e., limiting N unit productivity. The maximum productivity of N occurred in treatments with full P rate, especially when P fertilizer was applied as the PAPR. However, phosphorus yield forming action depended on weather conditions in the mead-season and P fertilizer rate. The first factor, affecting N and K supply to sugar beet during the mead-season, was responsible for the size of the beetroot, considered as the sugar storage. Any drought, negatively impacting its size, in turn decreases P yield forming action, which appears in the late-season. The maximal exploitation of sugar beet yielding potential is, therefore, possible provided water is not a factor limiting sugar beet growth in the mead-season and P in late-season. Nevertheless, in farming practice, the lack of favourable growth conditions should not be a reason for development a sugar beet fertilizing strategy, based on reduced P and K rates