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Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
Cell migration in fibreous extracellular matrix (ECM) is crucial to many physiological and pathological processes such as tissue regeneration, immune response and cancer progression. During migration, individual cells can generate active…
We devise experimental schemes able to mimic uniform and staggered magnetic fluxes acting on ultracold two-electron atoms, such as ytterbium atoms, propagating in a honeycomb lattice. The atoms are first trapped into two independent…
The technique presented here identifies tethered mould designs, optimised for growing cultured tissue with very highly-aligned cells. It is based on a microscopic biophysical model for polarised cellular hydrogels. There is an unmet need…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
Metamaterials present the possibility of artificially generating advanced functionalities through engineering of their internal structure. Artificial spin networks, in which a large number of nanoscale magnetic elements are coupled…
The Bose Hubbard model (BHM) of interacting bosons in a lattice has been a paradigm in many-body physics, and it exhibits a Mott insulator (MI)-superfluid (SF) transition at integer filling. Here a quantum simulator of the BHM using a…
We introduce a graphical method originating from the computer graphics domain that is used for the arbitrary and intuitive placement of cells over a two-dimensional manifold. Using a bitmap image as input, where the color indicates the…
A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…
Acoustic metamaterials are artificial structures, often lattice of resonators, with unusual properties. They can be engineered to stop wave propagation in specific frequency bands. Once manufactured, their dispersive qualities remain…
Spindles are self-organized microtubule-based structures that segregate chromosomes during cell division. The mass of the spindle is controlled by the balance between microtubule turnover and nucleation. The mechanisms that control the…
Vascular adhesion of circulating tumor cells (CTCs) is a key step in cancer spreading. If inflammation is recognized to favor the formation of vascular metastatic niches, little is known about the contribution of blood rheology to CTC…
The aim of this chapter is to provide a brief introduction into the basics of a top-down multilevel tumor dynamics modeling method primarily based on discrete entity consideration and manipulation. The method is clinically oriented, one of…
The calcium transport in biological systems is modelled as a reaction-diffusion process. Nonlinear calcium waves are then simulated using a stochastic cellular automaton whose rules are derived from the corresponding coupled partial…
We apply the cell merging method to a model shallow water problem with a permeable boundary. We use a cut cell approach which is more easily and systematically scalable with different shapes of boundaries. The novel cell merging method…
We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on the FCC lattice which takes explicitly into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer…
Particle-in-cell merging algorithms aim to resample dynamically the six-dimensional phase space occupied by particles without distorting substantially the physical description of the system. Whereas various approaches have been proposed in…
We demonstrate a method for manipulating small ensembles of vortices in multiply-connected superconducting structures. A micron-size magnetic particle attached to the tip of a silicon cantilever is used to locally apply magnetic flux…
A mathematical model for time development of metastases and their distribution in size and carrying capacity is presented. The model is used to theoretically investigate anti-cancer therapies such as surgery and chemical treatments…