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Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
In evolutionary robotics, jointly optimising the design and the controller of robots is a challenging task due to the huge complexity of the solution space formed by the possible combinations of body and controller. We focus on the…
Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional…
Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…
High-density microfluidics is becoming an important experimental platform for studying complex biological systems such as synthetic gene regulatory networks, molecular biocomputating of engineered cells, distributing rapid point-of-care…
Simulation design is the choice of locations in parameter space at which simulations are to be run and is the first step in building an emulator capable of quickly providing estimates of simulation results for arbitrary locations in the…
When designing systems that are complex, dynamic and stochastic in nature, simulation is generally recognised as one of the best design support technologies, and a valuable aid in the strategic and tactical decision making process. A…
We perform the linear stability analysis for a new model for poromechanical processes with inertia (formulated in mixed form using the solid deformation, fluid pressure, and total pressure) interacting with diffusing and reacting solutes…
Techniques for simulating molecules whose conformations satisfy constraints are presented. A method for selecting appropriate moves in Monte Carlo simulations is given. The resulting moves not only obey the constraints but also maintain…
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
Cosmological N-Body simulations have become an essential tool for studying formation of large scale structure. These simulations are computationally challenging even though the available computing power gets better every year. A number of…
The medical image analysis field has traditionally been focused on the development of organ-, and disease-specific methods. Recently, the interest in the development of more 20 comprehensive computational anatomical models has grown,…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
BioDynaMo is a biological processes simulator developed by an international community of researchers and software engineers working closely with neuroscientists. The authors have been working on gene expression, i.e. the process by which…
The computational treatment of many-electron systems capable of exchanging {electrons and nuclei} with the environment represents one of the outermost frontiers in simulation methodology. The exchanging process occurs in a large variety of…
Computational systems and methods are often being used in biological research, including the understanding of cancer and the development of treatments. Simulations of tumor growth and its response to different drugs are of particular…
Mathematical modelling of ionic electrodiffusion and water movement is emerging as a powerful avenue of investigation to provide new physiological insight into brain homeostasis. However, in order to provide solid answers and resolve…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
The diffuse medium in and around galaxies can exist in a multi-phase state: small, cold gas clouds contributing significantly to the total mass embedded in pressure equilibrium with a hotter, more diffuse volume-filling component. Modeling…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…