A5066663740- Lattice Boltzmann Simulation Studies
- Aerosol Filtration and Electrostatic Precipitation
- Bacterial biofilms and quorum sensing
- Microfluidic and Bio-sensing Technologies
- Blood properties and coagulation
- Micro and Nano Robotics
- Gene Regulatory Network Analysis
- Rheology and Fluid Dynamics Studies
- Pickering emulsions and particle stabilization
- Wastewater Treatment and Nitrogen Removal
- Inhalation and Respiratory Drug Delivery
- Coastal and Marine Dynamics
- Granular flow and fluidized beds
- Slime Mold and Myxomycetes Research
- Erythrocyte Function and Pathophysiology
- Advanced Multi-Objective Optimization Algorithms
- Fluid Dynamics and Vibration Analysis
- Acoustic Wave Phenomena Research
- Drilling and Well Engineering
- Numerical methods in engineering
- Scientific Computing and Data Management
- Gaussian Processes and Bayesian Inference
- Antimicrobial agents and applications
- Photoacoustic and Ultrasonic Imaging
- Ultrasonics and Acoustic Wave Propagation
University of Oxford
2019-2024
Newcastle University
2015-2021
National University of Singapore
2009-2015
Singapore-MIT Alliance for Research and Technology
2012-2014
The production of extracellular polymeric substance (EPS) is important for the survival biofilms. However, EPS costly bacteria and bacterial strains that produce (EPS+) grow in same environment as non-producers (EPS-) leading to competition between these nutrients space. outcome this likely be dependent on factors such initial attachment, rate, ambient nutrient levels quorum sensing. We use an Individual-based Model (IbM) study EPS+ EPS- by varying nature colonizers which can either form...
Accurate predictive modelling of the growth microbial communities requires credible representation interactions biological, chemical and mechanical processes. However, although biological processes are represented in a number Individual-based Models (IbMs) interaction mechanics is limited. Conversely, there mechanically sophisticated IbMs with only elementary biology chemistry. This study focuses on addressing these limitations by developing flexible IbM that can robustly combine physical...
We present NUFEB (Newcastle University Frontiers in Engineering Biology), a flexible, efficient, and open source software for simulating the 3D dynamics of microbial communities. The tool is based on Individual-based Modelling (IbM) approach, where microbes are represented as discrete units their behaviour changes over time due to variety processes. This approach allows us study population behaviours that emerge from interaction between individuals environment. built top classical molecular...
Deregulated metabolism is one of the hallmarks cancer. It well-known that tumour cells tend to metabolize glucose via glycolysis even when oxygen available and mitochondrial respiration functional. However, lower energy efficiency aerobic with respect makes this behaviour, namely Warburg effect, counter-intuitive, although it has now been recognized as source anabolic precursors. On other hand, there evidence oxygenated could be fuelled by exogenous lactate produced from glycolysis. We...
The ability to make credible simulations of open engineered biological systems is an important step towards the application scientific knowledge solve real-world problems in this challenging, complex engineering domain. An type design and management wastewater treatment systems. One crucial aspects biology approach study run a simulation communities. However, challenging because they often involve large number bacteria that ranges from order 1012 (a baby's microbiome) 1018 plant) individual...
The deformation and detachment of bacterial biofilm are related to the structural mechanical properties itself. Extracellular polymeric substances (EPS) play an important role on keeping stability biofilms. understanding mechanics can help reveal survival mechanisms under fluid shear provide insight about what flows might be needed remove in a cleaning cycle or for ship However, how EPS may affect its flow conditions remains elusive. To address this, coupled computational dynamic- discrete...
Structural and functional disorders of pulmonary cilia may result from genetic acquired insults. A two-dimensional numerical model based on the immersed boundary method coupled with projection is used to study flow physics muco-ciliary transport human respiratory tract under various abnormalities cilia. The effects beat pattern (CBP), ciliary length, immotile cilia, beating amplitude uncoordinated are investigated. As expected, mucus velocity decreases as reduces. windscreen wiper motion...
Individual based models (IbM) must transition from research tools to engineering tools. To make the we aspire develop large, three dimensional and physically biologically credible models. Biological credibility can be promoted by grounding, as far possible, biology in thermodynamics. Thermodynamic principles are known have predictive power microbial ecology. However, this turn requires a model that incorporates pH chemical speciation. Physical implies plausible mechanics connection with...
Individual-based (IB) modelling has been widely used for studying the emergence of complex interactions bacterial biofilms and their environment. We describe emulation calibration an expensive dynamic simulator IB model microbial communities. a combination multivariate linear models (DLM) Gaussian process to estimate parameters our emulators. The emulators incorporate smoothly varying nonstationary trend that is modelled as deterministic function explanatory variables while (GP) allowed...
Human pulmonary epithelial cells are protected by two layers of fluid—the outer watery periciliary liquid layer (PCL) and the uppermost non-Newtonian mucus (ML). Aerosols inhaled toxic particles trapped ML which must then be removed swiftly to avoid adverse health implications. Epithelial covered with cilia that beat rapidly within PCL. Such ciliary motion drives transport. Although can penetrate slightly inside assist movement, underlying PCL airway surface (ASL) is significant in pathogens...
The complex variables method with mapping function was extended to solve the linear acoustic wave scattering by an inclusion sharp/smooth corners in infinite ideal fluid domain. improved solutions of Helmholtz equation, shown as Bessel argument and fractional order function, were analytically obtained. Based on initial geometry well original physical vector can be transformed into corresponding expressions inside plane. As all vectors are calculated plane (η,η), this lead potential vast...
We investigate the feasibility of using a surrogate-based method to emulate deformation and detachment behaviour biofilm in response hydrodynamic shear stress. The influence force, growth rate viscoelastic parameters on patterns growth, structure resulting shape microbial biofilms was examined. develop statistical modelling approach this problem, combination Bayesian Poisson regression dynamic linear models for emulation. observe that force affects line with some literature. Sensitivity...
Bacterial habitats are often associated with fluid flow environments. twitching is important for initial bacterial colonization and biofilm formation. The existing research about bacteria largely experimental orientated. There a lack of models motility in shear flows, which could provide fundamental understanding how would be affected by properties such as number pili their distribution on the cell body environmental factors surface patterns. In this work, three-dimensional modelling...
Abstract We present NUFEB, a flexible, efficient, and open source software for simulating the 3D dynamics of microbial communities. The tool is based on Individual-based Modelling (IbM) approach, where microbes are represented as discrete units their behaviour changes over time due to variety processes. This approach allows us study population behaviours that emerge from interaction between individuals environment. NUFEB built top classical molecular simulator LAMMPS, which we extended with...