Shallow water equations with depth-dependent anisotropic porosity for subgrid-scale topography

This paper derives a novel formulation of the depth-averaged shallow water equations with anisotropic porosity for computational efficiency reasons. The aim is to run simulations on coarser grids while maintaining an acceptable accuracy through the introduction of porosity terms, which account for subgrid-scale effects. The porosity is divided into volumetric and areal porosities, which are assigned to the cell volume and the cell edges, respectively. The former represents the volume in the cell available to flow and the latter represents the area available to flow over an edge, hence introducing anisotropy. The porosity terms are variable in time in dependence of the water elevation in the cell and the cumulative distribution function of the unresolved bottom elevation. The main novelty of the equations is the formulation of the porosities which enables full inundation of the cell. The applicability of the equations is verified in five computational examples, dealing with dam break and rainfall-runoff simulations. Overall, good agreement between the model results and a high-resolution reference simulation has been achieved. The computational time decreased significantly: on average three orders of magnitude

Estimating the accuracy of the random walk simulation of mass transport

The mass transport processes always accompanies the flow phenomena and have attracted many researches. A lot of numerical methods have been developed to study them. These numerical methods can be classified into the Eulerian and the Lagrangian approaches. The Lagrangian approach has advantages in high stability and simplicity over the Eulerian approach, but suffers from heavy computational cost. In this paper, we are mainly concerned with the trade-offs between the accuracy and computational cost when applying the random walk method, which is a Lagrangian approach for examining the mass transport scenario. We introduce a linear model to assess the accuracy of the random walk method in several computational configurations. Studies on computational parameters, i.e. the size of time step and number of particles, are conducted with the focus on estimation of the longitudinal dispersion coefficient in steady flows. The results show that the proposed linear model can satisfactorily explain the computational accuracy, both in sample and out-of-sample. Furthermore, we find a constant dimensionless parameter, which quantifies a generic relationship between the accuracy and the number of particles regardless of the flow and diffusion conditions. This dimensionless parameter is of theoretic value and offers guidelines for choosing the correct computational parameters to achieve the required numerical accuracy.National Natural Science Foundation of China (51809219), State key Laboratory of Hydroscience and Engineering (sklhse-2019-B-02), Royal Academy of Engineering (Grant No. UUFRIP\100051), Ministry of Education and State Administration of Foreign Experts Affair

A Novel Slope Failure Operator for a Non-Equilibrium Sediment Transport Model

Complex transport mechanism and interaction between fluid and sediment make the mathematical and numerical modeling of sediment transport very challenging. Different types of models can lead to different results. This paper investigates a non-equilibrium sediment transport model based on the total load. In this type of model, it is assumed that a bed slide will occur if the bed slope reaches a critical angle. This is enabled by means of a slope failure operator. Existing slope failure operators usually suffer from the high computational cost and may fail at wet/dry interfaces. The main contribution of this work is the development of a novel slope failure operator for the total load transport model, based on a modified mass balance approach. The proposed approach is verified in three test cases, involving bank failure, dyke overtopping and a two-dimensional bank failure. It is shown that the proposed approach yields good agreement with analytical results and measurement data

An extracellular protein expression system in Escherichia coli implies potential application

Escherichia coli is commonly used as a host for the extracellular production of proteins. However, its secretion capacity is often limited to a frustratingly low level compared with other expression hosts, because E. coli has a complex cell envelope with two layers. We recently identified the catalytic domain of a cellulase (Cel-CD) from Bacillus sp. that can be secreted into the medium from recombinant E. coli in large quantities without its native signal peptide. By subcellular location analysis, we verified that the secretion was a two-step process via the SecB-dependent pathway through the inner membrane and an unknown pathway through the outer membrane. However, the N-terminal region of Cel-CD is polar and hydrophilic, which showed no similarities to other typical signal sequences. Random mutagenesis experiment suggested that the N-terminal sequence is a compromising result of transportation through inner and outer membranes. This is the first report that a non-classical signal peptide can guide recombinant proteins out of the cells from cytoplasm. Both the Cel-CD and its N-terminal sequence can serve as carriers for efficient extracellular production of select target proteins with a concentration from 101 to 691 mg/L in flask cultivation. This protein can degrading cellulose efficiently in the culture medium indicating a great potential. Therefore, a recombinant E.coli that can directly utilize cellulose as sole carbon source by fusion Cel-CD with a b-glucosidase was constructed. Recombinant strains were confirmed to use the amorphous cellulose as well as cellobiose as the sole carbon source for growth. Furthermore, both strains were engineered with poly (3-hydroxybutyrate) (PHB) synthesis pathway to demonstrate the production of biodegradable polyesters directly from cellulose materials without exogenously added cellulases. The results suggested that this system has a potential application in lignocellulosic biomass degradation and biochemical biofuel production. These guidelines have been prepared in the format that should be used for the abstract submission. Authors should replace the text of this template in order to prepare their abstracts. Fonts, sizes and spacing should be used as they are used in this document. Page size is US 8.5 inch x 11 inch, top and bottom margin 0.8 inches, left and right margin 0.8 inches. Body text should be written in Arial, 10 pt, single spacing. The Abstract, in English, should introduce the proposed paper’s subject, summarize its contents, explain any unique aspects, and clearly indicate the specific relevance to the themes of the Conference. Do not sub-divide the text into separate sections. References may be included at the bottom. Reference Exploring the N-terminal role of a heterologous protein in secreting out of Escherichia coli, Biotechnol Bioeng. 2016 Dec;113(12):2561-2567. doi: 10.1002/bit.26028. Epub 2016 Jun 14. Construction of cellulose-utilizing Escherichia coli based on a secretable cellulose, Microb Cell Fact. 2015 Oct 9;14:159. doi: 10.1186/s12934-015-0349-7

ClusterFormer: Clustering As A Universal Visual Learner

This paper presents CLUSTERFORMER, a universal vision model that is based on the CLUSTERing paradigm with TransFORMER. It comprises two novel designs: 1. recurrent cross-attention clustering, which reformulates the cross-attention mechanism in Transformer and enables recursive updates of cluster centers to facilitate strong representation learning; and 2. feature dispatching, which uses the updated cluster centers to redistribute image features through similarity-based metrics, resulting in a transparent pipeline. This elegant design streamlines an explainable and transferable workflow, capable of tackling heterogeneous vision tasks (i.e., image classification, object detection, and image segmentation) with varying levels of clustering granularity (i.e., image-, box-, and pixel-level). Empirical results demonstrate that CLUSTERFORMER outperforms various well-known specialized architectures, achieving 83.41% top-1 acc. over ImageNet-1K for image classification, 54.2% and 47.0% mAP over MS COCO for object detection and instance segmentation, 52.4% mIoU over ADE20K for semantic segmentation, and 55.8% PQ over COCO Panoptic for panoptic segmentation. For its efficacy, we hope our work can catalyze a paradigm shift in universal models in computer vision

Influences of laser heating parameters on thermophoretic enrichment of nanoparticles

Thermophoretic enrichment of particles has been recognised as an efficient way to concentrate nanovesicles in biomedical studies. Although some experimental and analytical studies have been undertaken to examine the thermophoretic accumulation mechanisms, few studies have been conducted to optimise the device design. This paper presents a detailed parametric study of a thermophoretic enrichment system, which sandwiches a microchamber containing particle/fluid mixture by a glass top, from where an infrared laser heat source is introduced, and a sapphire bottom, which has a high heat conductivity to prevent overheating. The influences of the laser spot radius, laser attenuation rate, nanoparticle size and laser power are investigated. The radius of the nanoparticle accumulation zone is found to be approximately 1.25 times the laser spot radius. A reduction in the laser attenuation length leads to a reduction of the time taken by the nanoparticles to reach the steady state, but an enlarged zone over which nanoparticles are concentrated. There exists an optimum range of the attenuation length, depending on the required size of the target area. We have also determined the threshold particle size, which decides whether the particle motion is convection-dominated or thermophoresis-dominated. Furthermore, an increase in the laser power reduces the accumulation time. These findings provide guidelines for the design of enrichment systems

30+ year evolution of Cu in the surface sediment of Lake Poyang, China.

Poyang Lake, the largest freshwater lake in China, is increasingly experiencing Cu crises. Combining field data, laboratory experiments, and long-term simulations, we retrieved 30 + year evolution of Cu in surface sediments (SCu). SCu evolution between 1983 and 2015 may be separated into two distinguishable periods. During the first period (1983-2003), SCu underwent a continuous increase at a mean rate of 1.80 mg/kg/yr; however, since 2003 it displayed a stepwise reduction tendency. The average SCu concentration of the entire lake in 2015 fell to 54.26 mg/kg, which is approximately 30.01% lower than that in 2003. The operation of Three Gorges Dam (TGD) markedly altered the river-lake relationship, pulled more deposited Cu along with sediment out toward the Yangtze River, and made the regions of high SCu emanate from the southeastern lake extend northwestward between 2003 and 2015. SCu in the reserves showed significant inter-annual variations, with the exception of the Jiangxi Whitebait Spawning Reserve (JWSR), where SCu generally has not been significantly impacted and has displayed no departure from the 30 + year mean of 30.57 mg/kg. The National Germplasm Reserve (NGR) and Nanjishan National Nature Reserve (NNNR) were detected with the highest SCu, with the peak concentrations, respectively, of 123.15 mg/kg and 103.1 mg/kg