UCL OpenFOAM Course Notes 2019

The UCL OpenFOAM Course was initiated by the Department of Mechanical Engineering, totally free and registered under UCL doctoral school. It aims to popularise OpenFOAM among research students and help beginners to get through the initial painful stage dealing with the unfamiliar operation environment, also an excellent chance to exchange simulation skills and generate collaborations. In 2019, the course was held during 26-28 June, with our lecturers and 55 students attended. It was fantastic to see so many conversations getting started, and to feel that our UK/London community is getting stronger. We received very positive feedback, and more importantly, strong interests from worldwide users who wanted but could not join us in London. Thereby, this document is published online to demonstrate what we have taught. We hope this will be helpful for a wider audience. In Chapter 1-4, we present step-by-step guideline for installing/using/understanding OpenFOAM; subsequently, our Appendixes provides advanced tutorials for various purposes

Different Types of Door-Opening Motions as Contributing Factors to Containment Failures in Hospital Isolation Rooms

10.1371/journal.pone.0066663PLoS ONE86-POLN

Absence of Detectable Influenza RNA Transmitted via Aerosol during Various Human Respiratory Activities – Experiments from Singapore and Hong Kong

Two independent studies by two separate research teams (from Hong Kong and Singapore) failed to detect any influenza RNA landing on, or inhaled by, a life-like, human manikin target, after exposure to naturally influenza-infected volunteers. For the Hong Kong experiments, 9 influenza-infected volunteers were recruited to breathe, talk/count and cough, from 0.1 m and 0.5 m distance, onto a mouth-breathing manikin. Aerosolised droplets exhaled from the volunteers and entering the manikin’s mouth were collected with PTFE filters and an aerosol sampler, in separate experiments. Virus detection was performed using an in-house influenza RNA reverse-transcription polymerase chain reaction (RT-PCR) assay. No influenza RNA was detected from any of the PTFE filters or air samples. For the Singapore experiments, 6 influenza-infected volunteers were asked to breathe (nasal/mouth breathing), talk (counting in English/second language), cough (from 1 m/0.1 m away) and laugh, onto a thermal, breathing manikin. The manikin’s face was swabbed at specific points (around both eyes, the nostrils and the mouth) before and after exposure to each of these respiratory activities, and was cleaned between each activity with medical grade alcohol swabs. Shadowgraph imaging was used to record the generation of these respiratory aerosols from the infected volunteers and their impact onto the target manikin. No influenza RNA was detected from any of these swabs with either team’s in-house diagnostic influenza assays. All the influenza-infected volunteers had diagnostic swabs taken at recruitment that confirmed influenza (A/H1, A/H3 or B) infection with high viral loads, ranging from 105-108 copies/mL (Hong Kong volunteers/assay) and 104–107 copies/mL influenza viral RNA (Singapore volunteers/assay). These findings suggest that influenza RNA may not be readily transmitted from naturally-infected human source to susceptible recipients via these natural respiratory activities, within these exposure time-frames. Various reasons are discussed in an attempt to explain these findings.published_or_final_versio

Airflow Dynamics of Coughing in Healthy Human Volunteers by Shadowgraph Imaging: An Aid to Aerosol Infection Control

Cough airflow dynamics have been previously studied using a variety of experimental methods. In this study, real-time, non-invasive shadowgraph imaging was applied to obtain additional analyses of cough airflows produced by healthy volunteers. Twenty healthy volunteers (10 women, mean age 32.2±12.9 years; 10 men, mean age 25.3±2.5 years) were asked to cough freely, then into their sleeves (as per current US CDC recommendations) in this study to analyze cough airflow dynamics. For the 10 females (cases 1–10), their maximum detectable cough propagation distances ranged from 0.16–0.55 m, with maximum derived velocities of 2.2–5.0 m/s, and their maximum detectable 2-D projected areas ranged from 0.010–0.11 m2, with maximum derived expansion rates of 0.15–0.55 m2/s. For the 10 males (cases 11–20), their maximum detectable cough propagation distances ranged from 0.31–0.64 m, with maximum derived velocities of 3.2–14 m/s, and their maximum detectable 2-D projected areas ranged from 0.04–0.14 m2, with maximum derived expansion rates of 0.25–1.4 m2/s

Identification of Ischemic Regions in a Rat Model of Stroke

Investigations following stroke first of all require information about the spatio-temporal dimension of the ischemic core as well as of perilesional and remote affected tissue. Here we systematically evaluated regions differently impaired by focal ischemia.Wistar rats underwent a transient 30 or 120 min suture-occlusion of the middle cerebral artery (MCAO) followed by various reperfusion times (2 h, 1 d, 7 d, 30 d) or a permanent MCAO (1 d survival). Brains were characterized by TTC, thionine, and immunohistochemistry using MAP2, HSP72, and HSP27. TTC staining reliably identifies the infarct core at 1 d of reperfusion after 30 min MCAO and at all investigated times following 120 min and permanent MCAO. Nissl histology denotes the infarct core from 2 h up to 30 d after transient as well as permanent MCAO. Absent and attenuated MAP2 staining clearly identifies the infarct core and perilesional affected regions at all investigated times, respectively. HSP72 denotes perilesional areas in a limited post-ischemic time (1 d). HSP27 detects perilesional and remote impaired tissue from post-ischemic day 1 on. Furthermore a simultaneous expression of HSP72 and HSP27 in perilesional neurons was revealed.TTC and Nissl staining can be applied to designate the infarct core. MAP2, HSP72, and HSP27 are excellent markers not only to identify perilesional and remote areas but also to discriminate affected neuronal and glial populations. Moreover markers vary in their confinement to different reperfusion times. The extent and consistency of infarcts increase with prolonged occlusion of the MCA. Therefore interindividual infarct dimension should be precisely assessed by the combined use of different markers as described in this study

Coaction of Spheroid-Derived Stem-Like Cells and Endothelial Progenitor Cells Promotes Development of Colon Cancer

Although some studies described the characteristics of colon cancer stem cells (CSCs) and the role of endothelial progenitor cells (EPCs) in neovascularization, it is still controversial whether an interaction exists or not between CSCs and EPCs. In the present study, HCT116 and HT29 sphere models, which are known to be the cells enriching CSCs, were established to investigate the roles of this interaction in development and metastasis of colon cancer. Compared with their parental counterparts, spheroid cells demonstrated higher capacity of invasion, higher tumorigenic and metastatic potential. Then the in vitro and in vivo relationship between CSCs and EPCs were studied by using capillary tube formation assay and xenograft models. Our results showed that spheroid cells could promote the proliferation, migration and tube formation of EPCs through secretion of vascular endothelial growth factor (VEGF). Meanwhile, the EPCs could increase tumorigenic capacity of spheroid cells through angiogenesis. Furthermore, higher microvessel density was detected in the area enriching cancer stem cells in human colon cancer tissue. Our findings indicate that spheroid cells possess the characteristics of cancer stem cells, and the coaction of CSCs and EPCs may play an important role in the development of colon cancer

Novel inhibitors of the calcineurin/NFATc hub - alternatives to CsA and FK506?

The drugs cyclosporine A (CsA) and tacrolimus (FK506) revolutionized organ transplantation. Both compounds are still widely used in the clinic as well as for basic research, even though they have dramatic side effects and modulate other pathways than calcineurin-NFATc, too. To answer the major open question - whether the adverse side effects are secondary to the actions of the drugs on the calcineurin-NFATc pathway - alternative inhibitors were developed. Ideal inhibitors should discriminate between the inhibition of (i) calcineurin and peptidyl-prolyl cis-trans isomerases (PPIases; the matchmaker proteins of CsA and FK506), (ii) calcineurin and the other Ser/Thr protein phosphatases, and (iii) NFATc and other transcription factors. In this review we summarize the current knowledge about novel inhibitors, synthesized or identified in the last decades, and focus on their mode of action, specificity, and biological effects

On the fundamental principles of waves propagating over complex geometry

In 2004 the Indian Ocean tsunami once again showed the world the destructive capabilities of these natural disasters. In this work this practical problem was abstracted to a simplified problem of waves propagating over complex geometry, specifically the processes involved in a solitary and leading depression wave interacting with a bottom seated semi-cylinder over uniform depth and shoaling topography. A purpose written Arbitrary-Lagrangian-Eulerian finite element code to solve the two-dimensional Navier-Stokes equation was developed. It utilised high performance libraries PETSc, Hypre and Triangle to perform simulations with approximately 8 million degrees of freedom across 256 cores on UCL’s supercomputer, Legion. The code was validated against five benchmark test cases and mesh convergence was shown. The code exhibited linear weak scaling and superlinear strong scaling and with this capability, these problems could be analysed using two tools; firstly, global conservation measures such momentum and energy. The rate of change of these integral measures were related to forces on obstacles and boundaries and agreement with model estimates was found even when the wave/boundary interactions were complex. Secondly, flow diagnostics such as the rate of strain and vorticity were used to characterise the velocity field. The large scale capability also allowed the free surface boundary layer to be captured which revealed an (weaker) oscillatory nature of that found at a rigid boundary. The code could not handle breaking and inundation, therefore experiments were carried out to study a depression wave as it interacts and breaks on a beach. Using a novel mechanism for generating isolated depression waves, general features such as extent and speed of recession and surge where characterised and it is noteworthy that the shoreline recession, a defining feature of shoaling depression waves, which was seen during the 2004 tsunami, was captured

The Transfer and Transport of a Passive Scalar Within an Isolated Array of Circular Cylinders in a Uniform Flow

The transfer and transport of a passive scalar T from an isolated array of circular cylinders of varying Reynolds number (Re = [1000, 333]) and solid fraction (0.0023 < ϕ < 0.3) in a uniform steady flow are investigated. This problem is an abstraction of the flow past emergent vegetation or marine aquaculture, in which passive contaminants are continuously generated. The upstream flow (T_{\infty} = 0) is uniform and incident on an array of N_{c} cylinders whose surfaces are set to T_{s} = 1. Three‐dimensional numerical simulations were carried out to investigate the mean and fluctuating Nusselt number of the individual cylinders and the array as a whole. To help interpret the numerical results a mathematical model, partly based on empirical relationships, is developed to predict the transfer. The transfer of the scalar from the array was found to increase when the Reynolds number was increased. As the solid fraction is increased the transfer increases, reaches a maximum, and then decreases. This is due to the collective effect of all the cylinders resulting in (i) a modification of the incident flow and (ii) a reduction in the scalar gradient between the cylinder surface and the locally incident flow on individual cylinders. These effects are highly dependent on the solid fraction. Additional simulations were carried out to decompose the contribution of these two processes on the transfer of individual cylinders