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A model of pattern formation in living systems is presented. The pattern is achieved by the sequential interaction of two signaling pathways. The coupling of the pattern to the (thick) epithelial sheet changes is given, when the Gauss…
The phase field model can accurately simulate the evolution of microstructures with complex morphologies, and it has been widely used for cell modeling in the last two decades. However, compared to other cellular models such as the…
Biological signaling is imagined as a combination of activation and transport. The former is triggered by local molecular interactions and the latter is the result of molecular diffusion. However, other fundamental physical principles of…
This paper describes and validates for the first time the dynamic modelling of Liquid Crystal (LC)-based planar multi-resonant cells, as well as its use as bias signals synthesis tool to improve their reconfigurability time. The dynamic LC…
In this work, simulation-based equations to calculate propagation constant in uniform or periodic structures (SES) are deduced and verified through simulations in various types of structures. The modeling of those structures are essentially…
The global scales of solar convection are studied through three-dimensional simulations of compressible convection carried out in spherical shells of rotating fluid which extend from the base of the convection zone to within 15 Mm of the…
From flocking birds to schooling fish, organisms interact to form collective dynamics across the natural world. Self-organization is present at smaller scales as well: cells interact and move during development to produce patterns in fish…
Biological systems are often modeled as a system of ordinary differential equations (ODEs) with time-invariant parameters. However, cell signaling events or pharmacological interventions may alter the cellular state and induce multi-mode…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
The manner in which signals propagate through dense granular systems in both space and time is not well understood. In order to learn more about this process, we carry out discrete element simulations of the system response to excitations…
Biological cells utilize membranes and liquid-like droplets, known as biomolecular condensates, to structure their interior. The interaction of droplets and membranes, despite being involved in several key biological processes, is so far…
Dynamic optical coherence tomography (DOCT) enables label-free functional imaging by capturing temporal OCT signal variations caused by intracellular and intratissue motions. However, the relationship between DOCT signals and the sample…
Continuum solvation models are becoming increasingly relevant in condensed matter simulations, allowing to characterize materials interfaces in the presence of wet electrified environments at a reduced computational cost with respect to all…
Accurately modeling multi-class cell topology is crucial in digital pathology, as it provides critical insights into tissue structure and pathology. The synthetic generation of cell topology enables realistic simulations of complex tissue…
The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay between chromosome-patterning biochemical ("epigenetic") marks…
We establish a framework for signal processing on product spaces of simplicial and cellular complexes. For simplicity, we focus on the product of two complexes representing time and space, although our results generalize naturally to…
There is some literature on the application of linear boundary element method (BEM) for real-time simulation of biological organs. However, literature is scant when it comes to the application of nonlinear BEM, although there is a…