A new biomanufacturing platform combining intracellular metabolic engineering of the oleaginous yeast
Recent advances in random walk particle tracking have enabled direct simulation of mixing and reactions by allowing the particles to interact with each other using a multipoint mass transfer scheme. The mass transfer scheme allows separation of mixing and spreading processes, among other advantages, but it is computationally expensive because its speed depends on the number of interacting particle pairs. This note explores methods for relieving the computational bottleneck caused by the mass transfer step, and we use these algorithms to develop a new parallel, interacting particle model. The new model is a combination of a sparse search algorithm and a novel domain decomposition scheme, both of which offer significant speedup relative to the reference case—even when they are executed serially. We combine the strengths of these methods to create a parallel particle scheme that is highly accurate and efficient with run times that scale as 1/
- PAR ID:
- 10453444
- Publisher / Repository:
- DOI PREFIX: 10.1029
- Date Published:
- Journal Name:
- Water Resources Research
- Volume:
- 55
- Issue:
- 4
- ISSN:
- 0043-1397
- Page Range / eLocation ID:
- p. 3556-3566
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
Yongjin J. Zhou (Ed.)more » « less
Abstract Yarrowia lipolytica and extracellular bioreaction engineering provides efficient bioconversion of plant oils/animal fats into high‐value products. However, predicting the hydrodynamics and mass transfer parameters is difficult due to the high agitation and sparging required to create dispersed oil droplets in an aqueous medium for efficient yeast fermentation. In the current study, commercial computational fluid dynamic (CFD) solver Ansys CFX coupled with the MUSIG model first predicts two‐phase system (oil/water and air/water) mixing dynamics and their particle size distributions. Then, a three‐phase model (oil, air, and water) utilizing dispersed air bubbles and a polydispersed oil phase was implemented to explore fermenter mixing, gas dispersion efficiency, and volumetric mass transfer coefficient estimations (kLa ). The study analyzed the effect of the impeller type, agitation speed, and power input on the tank's flow field and revealed that upward‐pumping pitched blade impellers (PBI) in the top two positions (compared to Rushton‐type) provided advantageous oil phase homogeneity and similar estimatedkLa values with reduced power. These results show good agreement with the experimental mixing andkLa data. -
more » « less
Abstract. Marine emissions of dimethyl sulfide (DMS) and the subsequent formation of its oxidation products methanesulfonic acid (MSA) and sulfuric acid (H2SO4) are well-known natural precursors of atmospheric aerosols, contributing to particle mass and cloud formation over ocean and coastal regions. Despite a long-recognized and well-studied role in the marine troposphere, DMS oxidation chemistry remains a work in progress within many current air quality and climate models, with recent advances exploring heterogeneous chemistry and uncovering previously unknown intermediate species. With the identification of additional DMS oxidation pathways and intermediate species that influence the eventual fate of DMS, it is important to understand the impact of these pathways on the overall sulfate aerosol budget and aerosol size distribution. In this work, we update and evaluate the DMS oxidation mechanism of the chemical transport model GEOS-Chem by implementing expanded DMS oxidation pathways in the model. These updates include gas- and aqueous-phase reactions, the formation of the intermediates dimethyl sulfoxide (DMSO) and methanesulfinic acid (MSIA), and cloud loss and aerosol uptake of the recently quantified intermediate hydroperoxymethyl thioformate (HPMTF). We find that this updated mechanism collectively decreases the global mean surface-layer gas-phase sulfur dioxide (SO2) mixing ratio by 40 % and enhances the sulfate aerosol (SO42-) mixing ratio by 17 %. We further perform sensitivity analyses exploring the contribution of cloud loss and aerosol uptake of HPMTF to the overall sulfur budget. Comparing modeled concentrations to available observations, we find improved biases relative to previous studies. To quantify the impacts of these chemistry updates on global particle size distributions and the mass concentration, we use the TwO-Moment Aerosol Sectional (TOMAS) aerosol microphysics module coupled to GEOS-Chem and find that changes in particle formation and growth affect the size distribution of aerosol. With this new DMS-oxidation scheme, the global annual mean surface-layer number concentration of particles with diameters smaller than 80 nm decreases by 16.8 %, with cloud loss processes related to HPMTF being mostly responsible for this reduction. However, the global annual mean number of particles larger than 80 nm (corresponding to particles capable of acting as cloud condensation nuclei, CCN) increases by 3.8 %, suggesting that the new scheme promotes seasonal particle growth to these sizes.
-
more » « less
Abstract Previous particle‐tracking (PT) algorithms for chemical reaction conceptualize each particle being composed of one species. Reactions occur by either complete or partial birth/death processes between interacting particles. Here we extend the method by placing any number of chemical species on each particle. The particle/particle interaction is limited to mass exchange. After exchange, reactions of any sort are carried out independently on each particle. The novel components of the algorithms are verified against analytic solutions where possible.
-
null (Ed.)Abstract We present a method for creating a new type of model particle that allows us to measure the mass transfer rate from the particle surface to the surrounding water. We use hollow glass spheres and sugar to create neutrally buoyant particles in a variety of molded shapes. These particles are an alternative to traditional gypsum objects for measuring mass transfer, with the important characteristic of being neutrally buoyant. This is an inexpensive method that allows for custom particle shapes to be manufactured with different densities. We test the utility of these particles by measuring their dissolution rates in homogeneous, isotropic turbulence in our laboratory turbulence tank. Our measurements fit our proposed model, and give a faster dissolution rate for rod-shaped particles than for disc-shaped ones. Graphic abstractmore » « less
-
Smoothed-particle hydrodynamics (SPH) is a mesh-free method used to simulate volumetric media in fluids, astrophysics, and solid mechanics. Visualizing these simulations is problematic because these datasets often contain millions, if not billions of particles carrying physical attributes and moving over time. Radial basis functions (RBFs) are used to model particles, and overlapping particles are interpolated to reconstruct a high-quality volumetric field; however, this interpolation process is expensive and makes interactive visualization difficult. Existing RBF interpolation schemes do not account for color-mapped attributes and are instead constrained to visualizing just the density field. To address these challenges, we exploit ray tracing cores in modern GPU architectures to accelerate scalar field reconstruction. We use a novel RBF interpolation scheme to integrate per-particle colors and densities, and leverage GPU-parallel tree construction and refitting to quickly update the tree as the simulation animates over time or when the user manipulates particle radii. We also propose a Hilbert reordering scheme to cluster particles together at the leaves of the tree to reduce tree memory consumption. Finally, we reduce the noise of volumetric shadows by adopting a spatially temporal blue noise sampling scheme. Our method can provide a more detailed and interactive view of these large, volumetric, time-series particle datasets than traditional methods, leading to new insights into these physics simulations.more » « less
