OpenPNM: A Pore Network Modeling Package

Pore network modeling is a widely used technique for simulating multiphase transport in porous materials, but there are very few software options available. This work outlines the OpenPNM package that was jointly developed by several porous media research groups to help address this gap. OpenPNM is written in Python using NumPy and SciPy for most mathematical operations, thus combining Python's ease of use with the performance necessary to perform large simulations. The package assists the user with managing and interacting with all the topological, geometrical, and thermophysical data. It also includes a suite of commonly used algorithms for simulating percolation and performing transport calculations on pore networks. Most importantly, it was designed to be highly flexible to suit any application and be easily customized to include user-specified pore-scale physics models. The framework is fast, powerful, and concise. An illustrative example is included that determines the effective diffusivity through a partially water-saturated porous material with just 29 lines of code

Exploring the Impact of Electrode Microstructure on Redox Flow Battery Performance Using a Multiphysics Pore Network Model

The redox flow battery is a promising energy storage technology for managing the inherent uncertainty of renewable energy sources. At present, however, they are too expensive and thus economically unattractive. Optimizing flow batteries is thus an active area of research, with the aim of reducing cost by maximizing performance. This work addresses microstructural electrode optimizations by providing a modeling framework based on pore-networks to study the multiphysics involved in a flow battery, with a specific focus on pore-scale structure and its impact on transport processes. The proposed pore network approach was extremely cheap in computation cost (compared to direct numerical simulation) and therefore was used for parametric sweeps to search for optimum electrode structures in a reasonable time. It was found that that increasing porosity generally helps performance by increasing the permeability and flow rate at a given pressure drop, despite reducing reactive surface area per unit volume. As a more nuanced structural study, it was found that aligning fibers in the direction of flow helps performance by increasing permeability but showed diminishing returns beyond slight alignment. The proposed model was demonstrated in the context of a hydrogen bromine flow battery but could be applied to any system of interest

Probing the Structure-Performance Relationship of Lithium-Ion Battery Cathodes Using Pore-Networks Extracted from Three-Phase Tomograms

Pore-scale simulations of Li-ion battery electrodes were conducted using both pore-network modeling and direct numerical simulation. Ternary tomographic images of NMC811 cathodes were obtained and used to create the pore-scale computational domains. A novel network extraction method was developed to manage the extraction of N-phase networks which was used to extract all three phases of NMC-811 electrode along with their interconnections Pore network results compared favorably with direct numerical simulations (DNS) in terms of effective transport properties of each phase but were obtained in significantly less time. Simulations were then conducted with combined diffusion-reaction to simulate the limiting current behavior. It was found that when considering only ion and electron transport, the electrode structure could support current densities about 300 times higher than experimentally observed values. Additional case studies were conducted to illustrate the necessity of ternary images which allow separate consideration of carbon binder domain and active material. The results showed a 24.4% decrease in current density when the carbon binder was treated as a separate phase compared to lumping the CBD and active material into a single phase. The impact of nanoporosity in the carbon binder phase was also explored and found to enhance the reaction rate by 16.8% compared to solid binder. In addition, the developed technique used 58 times larger domain volume than DNS which opens up the possibility of modelling much larger tomographic data sets, enabling representative areas of typically inhomogeneous battery electrodes to be modelled accurately, and proposes a solution to the conflicting needs of high-resolution imaging and large volumes for image-based modelling. For the first time, three-phase pore network modelling of battery electrodes has been demonstrated and evaluated, opening the path towards a new modelling framework for lithium ion batteries.The described here was financially supported by the University of Engineering and Technology Lahore, Pakistan as well as the Natural Science and Engineering Research Council (NSERC) of Canada and in the UK by the Faraday Institution (EP/R042012/1 and EP/R042063/1). Pablo A. García-Salaberri thanks the support from the STFC Early Career Award (ST/R006873/1) during his stay at the Electrochemical Innovation La

Degenerate recognition of MHC class I molecules with Bw4 and Bw6 motifs by a killer cell Ig-like receptor 3DL expressed by macaque NK cells

The killer cell immunoglobulin-like receptors (KIRs) expressed on the surface of natural killer (NK) cells recognize specific major histocompatibility complex class I (MHC-I) molecules and regulate NK cell activities against pathogen-infected cells and neoplasia. In human immunodeficiency virus (HIV) infection, survival is linked to host KIR and MHC-I genotypes. In the simian immunodeficiency virus (SIV) macaque model, however, the role of NK cells is unclear due to the lack of information on KIR-MHC interactions. Here, we describe the first characterization of a KIR-MHC interaction in pig-tailed macaques (Macaca nemestrina). Initially, we identified three distinct subsets of macaque NK cells that stained ex vivo with macaque MHC-I tetramers loaded with SIV peptides. We then cloned cDNAs corresponding to 15 distinct KIR3D alleles. One of these, KIR049-4, was an inhibitory KIR3DL that bound MHC-I tetramers and prevented activation, degranulation and cytokine production by macaque NK cells after engagement with specific MHC-I molecules on the surface of target cells. Furthermore, KIR049-4 recognized a broad range of MHC-I molecules carrying not only the Bw4 motif but also Bw6 and non-Bw4/Bw6 motifs. This degenerate, yet peptide-dependent, MHC reactivity differs markedly from the fine specificity of human KIRs

Crystallization and preliminary X-ray structural studies of a Melan-A pMHC-TCR complex

Melanocytes are specialized pigmented cells that are found in all healthy skin tissue. In certain individuals, diseased melanocytes can form malignant tumours, melanomas, which cause the majority of skin-cancer-related deaths. The melanoma-associated antigenic peptides are presented on cell surfaces via the class I major histocompatibility complex (MHC). Among the melanoma-associated antigens, the melanoma self-antigen A/melanoma antigen recognized by T cells (Melan-A/MART-1) has attracted attention because of its wide expression in primary and metastatic melanomas. Here, a preliminary X-ray crystal structural study of a soluble cognate T-cell receptor (TCR) in complex with a pMHC presenting the Melan-A peptide (ELAGIGILTV) is reported. The TCR and pMHC were refolded, purified and mixed together to form complexes, which were crystallized using the sitting-drop vapour-diffusion method. Single TCR–pMHC complex crystals were cryocooled and used for data collection. Diffraction data showed that these crystals belonged to space group P4(1)/P4(3), with unit-cell parameters a = b = 120.4, c = 81.6 Å. A complete data set was collected to 3.1 Å and the structure is currently being analysed

From DNA sequence to application: possibilities and complications

The development of sophisticated genetic tools during the past 15 years have facilitated a tremendous increase of fundamental and application-oriented knowledge of lactic acid bacteria (LAB) and their bacteriophages. This knowledge relates both to the assignments of open reading frames (ORF’s) and the function of non-coding DNA sequences. Comparison of the complete nucleotide sequences of several LAB bacteriophages has revealed that their chromosomes have a fixed, modular structure, each module having a set of genes involved in a specific phase of the bacteriophage life cycle. LAB bacteriophage genes and DNA sequences have been used for the construction of temperature-inducible gene expression systems, gene-integration systems, and bacteriophage defence systems. The function of several LAB open reading frames and transcriptional units have been identified and characterized in detail. Many of these could find practical applications, such as induced lysis of LAB to enhance cheese ripening and re-routing of carbon fluxes for the production of a specific amino acid enantiomer. More knowledge has also become available concerning the function and structure of non-coding DNA positioned at or in the vicinity of promoters. In several cases the mRNA produced from this DNA contains a transcriptional terminator-antiterminator pair, in which the antiterminator can be stabilized either by uncharged tRNA or by interaction with a regulatory protein, thus preventing formation of the terminator so that mRNA elongation can proceed. Evidence has accumulated showing that also in LAB carbon catabolite repression in LAB is mediated by specific DNA elements in the vicinity of promoters governing the transcription of catabolic operons. Although some biological barriers have yet to be solved, the vast body of scientific information presently available allows the construction of tailor-made genetically modified LAB. Today, it appears that societal constraints rather than biological hurdles impede the use of genetically modified LAB.

Pre-emptive and therapeutic adoptive immunotherapy for nasopharyngeal carcinoma: Phenotype and effector function of T cells impact on clinical response

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Integrity and Its Counterfeits: Implications for Economy, Business and Management

While the concept of integrity has long been explored by great philosophers and thinkers, its application in modern and postmodern business and economic contexts has been underdeveloped. Little have been done to address the vagueness and paradoxicality of integrity and its shadow reality of counterfeits. The thematic collection, which this paper complements, entitled ‘Integrity and Its Counterfeits: Implications for Economy, Business and Management’, makes a contribution towards filling the gap between the abstract concept of integrity and its application into business and economy, with a particular attention on the ambiguous, equivocal and diverse meanings of the concept, the complex and dynamic practicality of integrity, and the grey and dark areas of business out of integrity. This article introduces the background of the research theme and provides exemplary debates and emerging avenues of discussion on this topic

CD8+ T-cell specificity is compromised at a defined MHCI/CD8 affinity threshold

The CD8 co-receptor engages peptide-major histocompatibility complex class I (pMHCI) molecules at a largely invariant site distinct from the T-cell receptor (TCR)-binding platform and enhances the sensitivity of antigen-driven activation to promote effective CD8+ T-cell immunity. A small increase in the strength of the pMHCI/CD8 interaction (~1.5-fold) can disproportionately amplify this effect, boosting antigen sensitivity by up to two orders of magnitude. However, recognition specificity is lost altogether with more substantial increases in pMHCI/CD8 affinity (~10-fold). In this study, we used a panel of MHCI mutants with altered CD8-binding properties to show that TCR-mediated antigen specificity is delimited by a pMHCI/CD8 affinity threshold. Our findings suggest that CD8 can be engineered within certain biophysical parameters to enhance the therapeutic efficacy of adoptive T-cell transfer irrespective of antigen specificity