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 the Individual-based Modelling (IbM) approach, where microbes are represented as discrete units and their behaviour changes over time due to a variety of processes. This approach allows us to study population behaviours that emerge from the interaction between individuals and their environment. NUFEB is built on top of the classical molecular dynamics simulator LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator), which we extended with IbM features. A wide range of biological, physical and chemical processes are implemented to explicitly model microbial systems, with particular emphasis on biofilms. NUFEB is fully parallelised and allows for the simulation of large numbers of microbes (107 individuals and beyond). The parallelisation is based on a domain decomposition scheme that divides the domain into multiple sub-domains which are distributed to different processors. NUFEB also offers a collection of post-processing routines for the visualisation and analysis of simulation output. In this article, we give an overview of NUFEB’s functionalities and implementation details. We provide examples that illustrate the type of microbial systems NUFEB can be used to model and simulate.

Individual based Models (IbM) must transition from research tools to engineering tools. To make the transition we must aspire to develop large, three dimensional and physically and biologically credible models. Biological credibility can be promoted by grounding, as far as possible, the biology in thermodynamics. Thermodynamic principles are known to have predictive power in microbial ecology. However, this in turn requires a model that incorporates pH and chemical speciation. Physical credibility implies plausible mechanics and a connection with the wider environment. Here, we propose a step toward that ideal by presenting an individual based model connecting thermodynamics, pH and chemical speciation and environmental conditions to microbial growth for 5·10 5 individuals. We have showcased the model in two scenarios: a two functional group nitrification model and a three functional group anaerobic community. In the former, pH and connection to the environment had an important effect on the outcomes simulated. Whilst in the latter pH was less important but the spatial arrangements and community productivity (that is, methane production) were highly dependent on thermodynamic and reactor coupling. We conclude that if IbM are to attain their potential as tools to evaluate the emergent properties of engineered biological systems it will be necessary to combine the chemical, physical, mechanical and biological along the lines we have proposed. We have still fallen short of our ideals because we cannot (yet) calculate specific uptake rates and must develop the capacity for longer runs in larger models. However, we believe such advances are attainable. Ideally in a common, fast and modular platform. For future innovations in IbM will only be of use if they can be coupled with all the previous advances.

We present NUFEB, a flexible, efficient, and open source software for simulating the 3D dynamics of microbial communities. The tool is based on the Individual-based Modelling (IbM) approach, where microbes are represented as discrete units and their behaviour changes over time due to a variety of processes. This approach allows us to study population behaviours that emerge from the interaction between individuals and their environment. NUFEB is built on top of the classical molecular dynamics simulator LAMMPS, which we extended with IbM features. A wide range of biological, physical and chemical processes are implemented to explicitly model microbial systems. NUFEB is fully parallelised and allows for the simulation of large numbers of microbes (10 7 individuals and beyond). The parallelisation is based on a domain decomposition scheme that divides the domain into multiple sub-domains which are distributed to different processors. NUFEB also offers a collection of post-processing routines for the visualisation and analysis of simulation output. In this article, we give an overview of NUFEB's functionalities and implementation details. We provide examples that illustrate the type of microbial systems NUFEB can be used to model and simulate. Author summaryIndividual-based Models (IbM) are one of the most promising frameworks to study microbial communities, as they can explicitly describe the behaviour of each cell. The development of a general-purpose IbM solver should focus on efficiency and flexibility due to the unique characteristics of microbial systems. However, available tools for these purposes present significant limitations. Most of them only facilitate serial computing for single simulation, or only focus on biological processes, but do not model mechanical and chemical processes in detail. In this work, we introduce the IbM solver NUFEB May 17, 2019 1/19 that addresses these shortcoming. The tool facilitates the modelling of much needed biological, chemical, physical and individual microbes in detail, and offers the flexibility of model extension and customisation. NUFEB is also fully parallelised and allows for the simulation of large complex microbial system. In this paper, we first give an overview of NUFEB's functionalities and implementation details. Then, we use NUFEB to model and simulate a biofilm system with fluid dynamics, and a large and complex biofilm system with multiple microbial functional groups and multiple nutrients. 1 This is a PLOS Computational Biology Software paper. 28 biological, chemical and physical processes, or sometimes it may be a simple model that 29 describes mono-functional group or focuses on a few processes. Thus, it is important for 30 the solver to be highly customisable (for building IbM) and extendible (with new IbM 31 features). Second, the solver should be scalable. Simulation of large microbial 32 communities is difficult since they contain a very high number of individuals. Different 33 modelling strategies have been proposed to overcome this limitation, inclu...

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Moving Particle Semi-implicit (MPS) is a Lagrangian, meshfree, computational method for fluid simulation. This work focus on using GPU clusters for MPS simulations. To accomplish this, we have to deal with two different levels of parallelism: one responsible for making different cluster nodes work together in a distributed memory system, and the other using the parallelism of GPU devices available on each node. First we present a performance comparison between single-node GPU and single-node multithreaded CPU implementations to investigate GPU speedups. Further, we analyze the performance in a multi-node GPU cluster environment.

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This paper discusses the prerequisites and the technical aspects of an innovative real-time simulator for DP-shuttle tanker and FPSO offshore connection operation. This simulator was developed by means of a partnership between the University of Sao Paulo and Petrobras. The software is based on the TPN (Numerical Offshore Tank) numerical code which had several modifications, in order perform real-time simulations. The mathematical models considered in the simulator and the computer architecture (hardware and software) will be presented.

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